diff --git a/cl-base.owl b/cl-base.owl index 3565ddfe4..006392d2f 100644 --- a/cl-base.owl +++ b/cl-base.owl @@ -22,7 +22,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + An ontology of cell types. Cell Ontology @@ -37,8 +37,8 @@ - See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. - 2024-05-15 + See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo. + 2024-07-10 @@ -122,13 +122,17 @@ - + + + - + + + @@ -138,6 +142,7 @@ 2023-03-31T09:17:34Z a subset of general classes related to blood and the immune system, primarily of hematopoietic origin blood_and_immune_upper_slim + @@ -147,6 +152,7 @@ a subset of general classes related to specific cell types in the eye. eye_upper_slim + @@ -156,6 +162,7 @@ a subset of general classes of cell types in the cell ontology. general_cell_types_upper_slim + @@ -166,6 +173,7 @@ 2023-11-22T11:18:57Z a subset of general classes related to specific cell types in the kidney kidney_upper_slim + @@ -212,6 +220,12 @@ + + + + + + @@ -483,6 +497,12 @@ + + + + + + @@ -3797,15 +3817,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + - + - @@ -3822,17 +3841,10 @@ Covers cells actively being cultured or stored in a quiescent state for future u An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -4103,12 +4115,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + - + @@ -4144,20 +4156,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + - - - - - - An epithelial cell of the pancreas. BTO:0000028 ZFA:0009045 @@ -5735,8 +5740,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -6415,7 +6426,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -10208,9 +10218,29 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + + + + + + + + + + + An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption. + + PMID:25422372 ZFA:0009143 + All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys. brush border epithelial cell @@ -11799,6 +11829,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -11811,9 +11842,10 @@ The modern definition of neurosecretion has evolved to include the release of an CALOHA:TS-2168 FMA:62499 alveolar epithelial cell + pneumocyte pneumonocyte - pneumocyte + pulmonary alveolar epithelial cell @@ -11821,6 +11853,13 @@ The modern definition of neurosecretion has evolved to include the release of an An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates. GOC:tfm PMID:20054144 + PMID:29463737 + + + + + pneumocyte + PMID:32491474 @@ -14618,20 +14657,20 @@ The modern definition of neurosecretion has evolved to include the release of an - + A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods. somatic stem cell FBbt:00004903 follicle stem cell (sensu Arthropoda) - + - + https://github.com/obophenotype/cell-ontology/issues/1943 @@ -15759,7 +15798,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -15772,14 +15811,14 @@ The modern definition of neurosecretion has evolved to include the release of an FBbt:00004904 follicle cell of egg chamber - + - + @@ -16430,6 +16469,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. BTO:0000542 CALOHA:TS-0729 @@ -17234,19 +17279,19 @@ The modern definition of neurosecretion has evolved to include the release of an - + A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed. ZFA:0009242 primary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -17361,19 +17406,19 @@ The modern definition of neurosecretion has evolved to include the release of an - + A neuron of teleosts that develops later than a primary neuron, typically during the larval stages. ZFA:0009246 secondary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -23933,12 +23978,36 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + + + + + + + + + + + + An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. ZFA:0009286 window cell - fenestrated cell + fenestrated endothelial cell + + + + An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. + DOI:10.1007/978-3-211-99390-3_133 + @@ -25776,7 +25845,7 @@ radial glial cells acting as neural progenitors throughout life. Obsoleted as this term probably resulted from a confusion. Hemocytes are either derived from the embryonic head mesoderm ("embryonic hemocytes") or from the larval lymph gland ("lymph gland hemocytes"), not from an "embryonic gland". - embryonic gland hemocyte + obsolete embryonic gland hemocyte true @@ -26518,7 +26587,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -26549,7 +26618,7 @@ radial glial cells acting as neural progenitors throughout life. FMB cone bipolar cell type 2 cone bipolar cell (sensu Mus) - + @@ -26569,7 +26638,7 @@ radial glial cells acting as neural progenitors throughout life. - + PMID:27565351 @@ -44917,7 +44986,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. - 2012-01-12T09:58:38Z + 2012-01-12T09:58:38Z 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro @@ -44954,7 +45023,7 @@ radial glial cells acting as neural progenitors throughout life. A connective tissue cell found in bone. - 2011-11-16T04:28:16Z + 2011-11-16T04:28:16Z bone cell @@ -46293,7 +46362,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative @@ -48104,7 +48173,7 @@ radial glial cells acting as neural progenitors throughout life. An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative. - 2010-04-26T10:14:16Z + 2010-04-26T10:14:16Z c- Kit-positive erythroid progenitor cell Markers found on mouse cells. Kit-positive erythroid progenitor cell @@ -48170,7 +48239,7 @@ radial glial cells acting as neural progenitors throughout life. A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative. - 2010-01-13T03:19:22Z + 2010-01-13T03:19:22Z Markers are for human cells. According to different research groups, CD45RA is present or absent on this cell population. CD34-positive, CD38-positive granulocyte monocyte progenitor @@ -48290,7 +48359,7 @@ radial glial cells acting as neural progenitors throughout life. A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative. - 2010-01-13T03:19:28Z + 2010-01-13T03:19:28Z Markers are found on mouse cells. Kit-positive granulocyte monocyte progenitor @@ -48353,7 +48422,7 @@ radial glial cells acting as neural progenitors throughout life. An erythroid progenitor cell that is CD34-positive and is GlyA-negative. - 2010-04-26T10:14:30Z + 2010-04-26T10:14:30Z FMA:83517 Cell markers associated with human cells. CD34-positive, GlyA-negative erythroid progenitor cell @@ -48414,7 +48483,7 @@ radial glial cells acting as neural progenitors throughout life. A proerythoblast that is CD34-negative and GlyA-negative. - 2010-04-26T10:31:50Z + 2010-04-26T10:31:50Z Cell surface markers are associated with human cells. CD34-negative, GlyA-negative proerythroblast @@ -48488,7 +48557,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative. - 2010-01-13T03:43:10Z + 2010-01-13T03:43:10Z Markers are associated with human cell type. CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell @@ -48592,7 +48661,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low. - 2010-01-13T03:43:12Z + 2010-01-13T03:43:12Z Markers are associated with mouse cells. Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell @@ -48661,7 +48730,7 @@ radial glial cells acting as neural progenitors throughout life. A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell. - 2010-01-14T03:25:15Z + 2010-01-14T03:25:15Z Markers are found on mouse cells. Kit-low, CD34-positive eosinophil progenitor cell @@ -48718,7 +48787,7 @@ radial glial cells acting as neural progenitors throughout life. A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell. - 2010-01-14T03:25:17Z + 2010-01-14T03:25:17Z Markers are associated with human cells. CD34-positive, CD38-positive eosinophil progenitor cell @@ -48779,7 +48848,7 @@ radial glial cells acting as neural progenitors throughout life. A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. - 2010-01-19T02:51:58Z + 2010-01-19T02:51:58Z MDP macrophage dendritic cell progenitor @@ -48979,7 +49048,7 @@ radial glial cells acting as neural progenitors throughout life. A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha. - 2010-01-19T03:39:30Z + 2010-01-19T03:39:30Z pre-conventional dendritic cell @@ -49057,7 +49126,7 @@ radial glial cells acting as neural progenitors throughout life. A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative. - 2010-01-26T02:43:40Z + 2010-01-26T02:43:40Z murine MDP Markers are associated with mouse cells. Kit-positive macrophage dendritic cell progenitor @@ -49147,7 +49216,7 @@ radial glial cells acting as neural progenitors throughout life. A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive. - 2010-04-26T10:31:56Z + 2010-04-26T10:31:56Z Markers are associated with mouse cells. Kit-low proerythroblast @@ -49207,7 +49276,7 @@ radial glial cells acting as neural progenitors throughout life. A basophilic erythroblast that is GlyA-positive. - 2010-04-26T10:41:15Z + 2010-04-26T10:41:15Z Markers are associated with human cells. GlyA-positive basophilic erythroblast @@ -49287,7 +49356,7 @@ radial glial cells acting as neural progenitors throughout life. A basophilic erythroblast that is Lyg 76-high and is Kit-negative. - 2010-04-26T10:41:22Z + 2010-04-26T10:41:22Z Cell surface markers are associated with mouse cells. Kit-negative, Ly-76 high basophilic erythroblast @@ -49367,7 +49436,7 @@ radial glial cells acting as neural progenitors throughout life. A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative. - 2010-04-26T10:53:11Z + 2010-04-26T10:53:11Z late basophilic and polychromatophilic erythroblast Kit-negative, Ly-76 high polychromatophilic erythroblast @@ -49427,7 +49496,7 @@ radial glial cells acting as neural progenitors throughout life. A polychromatiic erythroblast that is Gly-A-positive and CD71-low. - 2010-04-26T10:53:16Z + 2010-04-26T10:53:16Z Cell surface markers are associated with human cells. CD71-low, GlyA-positive polychromatic erythroblast @@ -49517,7 +49586,7 @@ radial glial cells acting as neural progenitors throughout life. An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative. - 2010-04-26T11:04:15Z + 2010-04-26T11:04:15Z Cell surface markers associated with mouse cells. Kit-negative, Ly-76 high orthochromatophilic erythroblasts @@ -49577,7 +49646,7 @@ radial glial cells acting as neural progenitors throughout life. An erythroblast that is GlyA-positive and CD71-negative. - 2010-04-26T11:04:21Z + 2010-04-26T11:04:21Z Markers associated with human cells. CD71-negative, GlyA-positive orthochromatic erythroblast @@ -49627,7 +49696,7 @@ radial glial cells acting as neural progenitors throughout life. A reticulocyte that is Ly76-high and is Kit-negative. - 2010-04-26T11:37:00Z + 2010-04-26T11:37:00Z Marker associated with mouse cells. Ly-76 high reticulocyte @@ -49677,7 +49746,7 @@ radial glial cells acting as neural progenitors throughout life. A reticulocyte that is GlyA-positive. - 2010-04-26T11:48:25Z + 2010-04-26T11:48:25Z Markers is associated with human cells. GlyA-positive reticulocytes @@ -49727,7 +49796,7 @@ radial glial cells acting as neural progenitors throughout life. An enucleate erythrocyte that is GlyA-positive. - 2010-04-26T11:51:22Z + 2010-04-26T11:51:22Z Marker is associated with human cell types. GlyA-positive erythrocyte @@ -49777,7 +49846,7 @@ radial glial cells acting as neural progenitors throughout life. An enucleate erythrocyte that is Lyg-76-high. - 2010-04-26T11:51:27Z + 2010-04-26T11:51:27Z Marker is associated with mouse cell types. Ly-76 high positive erythrocyte @@ -49847,7 +49916,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface. - 2010-04-26T02:39:09Z + 2010-04-26T02:39:09Z Markers are associated with human cell type. CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell @@ -49957,7 +50026,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low. - 2010-04-26T02:39:15Z + 2010-04-26T02:39:15Z Markers are associated with mouse cells. Kit-positive megakaryocyte progenitor cell @@ -50027,7 +50096,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative. - 2010-04-26T03:52:47Z + 2010-04-26T03:52:47Z Markers are commonly associated with human cells. CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell @@ -50097,7 +50166,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive. - 2010-04-26T03:59:22Z + 2010-04-26T03:59:22Z Markers are commonly associated with human cells. CD34-negative, CD41-positive, CD42-positive megakaryocyte cell @@ -50157,7 +50226,7 @@ radial glial cells acting as neural progenitors throughout life. A megakaryocyte cell with is CD9-positive and CD41-positive. - 2010-04-27T10:39:07Z + 2010-04-27T10:39:07Z Markers are commonly associated with mouse cells. CD9-positive, CD41-positive megakaryocyte cell @@ -50276,7 +50345,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa - 2010-04-27T12:46:33Z + 2010-04-27T12:46:33Z BMCP There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. @@ -50351,7 +50420,7 @@ radial glial cells acting as neural progenitors throughout life. A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low. - 2010-04-27T01:22:19Z + 2010-04-27T01:22:19Z Fc-epsilon RIalpha-low mast cell progenitor @@ -50417,7 +50486,7 @@ radial glial cells acting as neural progenitors throughout life. A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high. - 2010-04-27T01:22:32Z + 2010-04-27T01:22:32Z Markers are associated with mouse cells. Fc-epsilon RIalpha-high basophil progenitor cell @@ -50468,7 +50537,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -50512,7 +50581,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -50571,7 +50640,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative. - 2010-01-08T09:19:25Z + 2010-01-08T09:19:25Z ST stem cell ST-HSC Markers are associated with mouse cells. These cells are also reportedly CD11b-low and CD90-low. @@ -50641,7 +50710,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. - 2010-01-08T09:19:28Z + 2010-01-08T09:19:28Z LT stem cell LT-HSC Markers are associated with mouse cells. @@ -50723,7 +50792,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative. - 2010-01-08T11:16:33Z + 2010-01-08T11:16:33Z Markers are associated with mouse cells. Slamf1-negative multipotent progenitor cell @@ -50793,7 +50862,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive. - 2010-01-08T11:16:35Z + 2010-01-08T11:16:35Z KSL cell Markers are associated with mouse cells. Slamf1-positive multipotent progenitor cell @@ -50857,7 +50926,7 @@ radial glial cells acting as neural progenitors throughout life. Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive. - 2009-10-20T02:20:43Z + 2009-10-20T02:20:43Z memory alpha beta IEL CD2-positive, CD5-positive, CD44-positive alpha-beta intraepithelial T cell @@ -50967,7 +51036,7 @@ radial glial cells acting as neural progenitors throughout life. A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production. - 2009-10-29T04:01:27Z + 2009-10-29T04:01:27Z T(FH) Tfh follicular B helper T cell @@ -51105,7 +51174,7 @@ radial glial cells acting as neural progenitors throughout life. A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell. - 2009-10-29T04:09:16Z + 2009-10-29T04:09:16Z immature NK T cell stage I @@ -51173,7 +51242,7 @@ radial glial cells acting as neural progenitors throughout life. A CD24-low, CD44-negative, NK1.1-negative NK T cell. - 2009-10-29T04:13:43Z + 2009-10-29T04:13:43Z NKT.44-NK1.1-.Th NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org. immature NK T cell stage II @@ -51254,7 +51323,7 @@ radial glial cells acting as neural progenitors throughout life. A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell. - 2009-10-29T04:14:48Z + 2009-10-29T04:14:48Z NKT.44+.NK1.1-.Th immature NK T cell stage III @@ -51333,7 +51402,7 @@ radial glial cells acting as neural progenitors throughout life. A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell. - 2009-10-29T04:17:38Z + 2009-10-29T04:17:38Z NKT.44+.NK1.1-.Th immature NK T cell stage IV @@ -51408,7 +51477,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative. - 2010-01-12T11:14:15Z + 2010-01-12T11:14:15Z Cell markers are associated with human hematopoietic multipotent progenitor cells. CD34-positive, CD38-negative multipotent progenitor cell @@ -51492,7 +51561,7 @@ radial glial cells acting as neural progenitors throughout life. A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative. - 2010-04-27T01:22:38Z + 2010-04-27T01:22:38Z Markers are associated with mouse cells. Kit-positive, integrin beta7-high basophil mast progenitor cell @@ -51595,7 +51664,7 @@ radial glial cells acting as neural progenitors throughout life. A pro-B cell that is CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive. - 2010-04-28T10:50:07Z + 2010-04-28T10:50:07Z fraction A pre pro B cell @@ -51724,7 +51793,7 @@ radial glial cells acting as neural progenitors throughout life. A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage. - 2010-04-28T11:19:11Z + 2010-04-28T11:19:11Z Markers are commonly associated with human cells. These cells are also reportedly CD21-negative. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. early pro-B cell @@ -51789,7 +51858,7 @@ radial glial cells acting as neural progenitors throughout life. A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative. - 2010-04-28T11:56:21Z + 2010-04-28T11:56:21Z Fr. B Fraction B Markers are commonly associated with mouse cells. These cells are also reportedly RAG1-positive and RAG2-positive. @@ -51871,7 +51940,7 @@ radial glial cells acting as neural progenitors throughout life. A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive. - 2010-04-28T12:06:06Z + 2010-04-28T12:06:06Z Late pro-B cells are also reportedly CD10-positive, CD20-negative, CD21-negative, and TdT-positive. Transcription factors: PU.1-positive, Ikaros-positive, E2A-positive, and PAX5-positive. late pro-B cell @@ -51986,7 +52055,7 @@ radial glial cells acting as neural progenitors throughout life. A precursor B cell that is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain. - 2010-04-28T02:04:01Z + 2010-04-28T02:04:01Z Fraction C fraction C precursor B cell @@ -52085,7 +52154,7 @@ radial glial cells acting as neural progenitors throughout life. A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive. - 2010-04-28T02:13:46Z + 2010-04-28T02:13:46Z Fr. C' Fraction C-prime fraction C' precursor B cell @@ -52145,7 +52214,7 @@ radial glial cells acting as neural progenitors throughout life. A pre-BCR positive B cell that is CD38-high. - 2010-04-28T02:27:47Z + 2010-04-28T02:27:47Z large pre-B cell type I Markers are associated with human cells. CD38-high pre-BCR positive cell @@ -52257,7 +52326,7 @@ radial glial cells acting as neural progenitors throughout life. A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive. - 2010-04-28T02:55:16Z + 2010-04-28T02:55:16Z Fr. D fraction D pre-B cell Fraction D precursor B cells are also reportedly CD24-positive and sIgD-negative. @@ -52322,7 +52391,7 @@ radial glial cells acting as neural progenitors throughout life. A small pre-B cell that is CD22-positive and CD38-low. - 2010-04-28T03:04:48Z + 2010-04-28T03:04:48Z small pre-B cell Markers are associated with human cell. RAG expression maybe diminishing. CD22-positive, CD38-low small pre-B cell @@ -52416,7 +52485,7 @@ radial glial cells acting as neural progenitors throughout life. An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive. - 2010-04-28T03:13:47Z + 2010-04-28T03:13:47Z Markers associated with mouse cells. These cells are also reportedly sIgD-negative. fraction E immature B cell @@ -52498,7 +52567,7 @@ radial glial cells acting as neural progenitors throughout life. An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high. - 2010-04-28T03:19:14Z + 2010-04-28T03:19:14Z Markers are associated with human cell type. CD38-negative immature B cell @@ -52605,7 +52674,7 @@ radial glial cells acting as neural progenitors throughout life. A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative. - 2010-04-30T03:01:48Z + 2010-04-30T03:01:48Z fraction F mature B cell @@ -52666,7 +52735,7 @@ radial glial cells acting as neural progenitors throughout life. A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive. - 2010-06-05T08:25:41Z + 2010-06-05T08:25:41Z CD16- monocyte CD16-negative monocyte @@ -52771,7 +52840,7 @@ radial glial cells acting as neural progenitors throughout life. A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive. - 2010-06-05T08:25:44Z + 2010-06-05T08:25:44Z Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Also, this cell-type is sometimes described as being Gr1-negative. Gr1-low non-classical monocyte @@ -52815,7 +52884,7 @@ radial glial cells acting as neural progenitors throughout life. A conventional thymic dendritic cell that is CD8alpha-positive. - 2010-06-07T02:48:36Z + 2010-06-07T02:48:36Z CD8alpha-alpha-positive thymic conventional dendritic cell DC.8+.Th @@ -52850,7 +52919,7 @@ radial glial cells acting as neural progenitors throughout life. A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes. - 2010-06-22T10:46:12Z + 2010-06-22T10:46:12Z melanophage @@ -52913,7 +52982,7 @@ radial glial cells acting as neural progenitors throughout life. A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed. - 2010-06-22T11:18:44Z + 2010-06-22T11:18:44Z T helper cells type 9 T(H)-9 cell Th9 @@ -52964,14 +53033,12 @@ radial glial cells acting as neural progenitors throughout life. - A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. + A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. - 2010-06-23T04:37:54Z + 2010-06-23T04:37:54Z BTO:0000780 FMA:62500 - AT1 - ATI lung type 1 cells membranous pneumocytes pulmonary alveolar type I cell @@ -52982,18 +53049,41 @@ radial glial cells acting as neural progenitors throughout life. type 1 pneumocyte type I alveolar cells type I alveolar epithelial cells + type I pneumocyte + AT1 + ATI - type I pneumocyte + pulmonary alveolar type 1 cell - A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. + A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. GOC:tfm PMID:20054144 + PMID:29463737 http://www.copewithcytokines.de + + + + type 1 pneumocyte + PMID:32491474 + + + + + AT1 + PMID:29463737 + + + + + + ATI + + @@ -53015,7 +53105,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -53025,15 +53114,12 @@ radial glial cells acting as neural progenitors throughout life. - A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. + A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. - 2010-06-24T12:04:13Z + 2010-06-24T12:04:13Z BTO:0000538 FMA:62501 - AT2 - ATII - TII cuboidal type II cell granular pneumocyte great alveolar cell @@ -53044,20 +53130,44 @@ radial glial cells acting as neural progenitors throughout life. type II alveolar cell type II alveolar epithelial cell type II alveolocyte + type II pneumocyte + AT2 + ATII + TII lung type II cell - type II pneumocyte + pulmonary alveolar type 2 cell - A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. + A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli. GOC:tfm ISBN:0412046911 + PMID:36138472 PMID:8540632 http://www.copewithcytokines.de + + + + type II pneumocyte + PMID:32491474 + + + + + AT2 + PMID:36138472 + + + + + + ATII + + @@ -53092,7 +53202,7 @@ radial glial cells acting as neural progenitors throughout life. A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. - 2010-06-24T03:16:29Z + 2010-06-24T03:16:29Z BTO:0000028 CALOHA:TS-0737 FMA:63032 @@ -53142,7 +53252,7 @@ radial glial cells acting as neural progenitors throughout life. A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane. - 2010-06-28T08:24:30Z + 2010-06-28T08:24:30Z FMA:14118 Kultschitzky cell of bronchiole bronchiolar Kulchitsky cell @@ -53185,7 +53295,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell that produces glucagon. - 2010-09-10T10:48:54Z + 2010-09-10T10:48:54Z FMA:62939 type A enteroendocrine cell @@ -53206,7 +53316,7 @@ radial glial cells acting as neural progenitors throughout life. Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. - 2010-06-28T08:36:15Z + 2010-06-28T08:36:15Z BTO:0001032 FMA:14146 Purkinje cell fiber @@ -53232,7 +53342,7 @@ radial glial cells acting as neural progenitors throughout life. Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices. - 2010-06-29T09:58:13Z + 2010-06-29T09:58:13Z FMA:67909 type 2 vestibular hair cell type 2 vestibular sensory cell @@ -53255,7 +53365,7 @@ radial glial cells acting as neural progenitors throughout life. Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending. - 2010-06-29T09:58:19Z + 2010-06-29T09:58:19Z FMA:62352 type 1 vestibular hair cell type 1 vestibular sensory cell @@ -53297,7 +53407,7 @@ radial glial cells acting as neural progenitors throughout life. Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type. - 2010-06-29T11:07:25Z + 2010-06-29T11:07:25Z columnar cell BTO:0002484 FMA:63638 @@ -53330,7 +53440,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. - 2010-06-29T11:41:37Z + 2010-06-29T11:41:37Z pacemaker cell BTO:0004190 FMA:67101 @@ -53361,7 +53471,7 @@ radial glial cells acting as neural progenitors throughout life. Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. - 2010-06-29T02:39:32Z + 2010-06-29T02:39:32Z FMA:67142 transitional myocyte @@ -53382,7 +53492,7 @@ radial glial cells acting as neural progenitors throughout life. The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). - 2010-06-29T11:50:47Z + 2010-06-29T11:50:47Z FMA:67111 myocardial endocrine cell @@ -53405,7 +53515,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -53414,7 +53524,7 @@ radial glial cells acting as neural progenitors throughout life. Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known. - 2010-06-29T03:22:46Z + 2010-06-29T03:22:46Z pulmonary brush cell brush cell of tracheobronchial tree @@ -53433,6 +53543,17 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + @@ -53443,7 +53564,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell derived from endoderm. - 2010-06-29T03:38:14Z + 2010-06-29T03:38:14Z FMA:69075 ZFA:0009383 endo-epithelial cell @@ -53488,7 +53609,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -53533,7 +53654,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cell derived from mesoderm or mesenchyme. - 2010-06-29T03:49:14Z + 2010-06-29T03:49:14Z FMA:69076 ZFA:0009388 epithelial mesenchymal cell @@ -53590,7 +53711,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. - 2010-06-30T08:49:43Z + 2010-06-30T08:49:43Z FMA:63099 ZFA:0009380 @@ -53648,7 +53769,7 @@ radial glial cells acting as neural progenitors throughout life. A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. - 2010-06-30T08:49:52Z + 2010-06-30T08:49:52Z FMA:62455 ZFA:0005740 centroacinar cell of Langerhans @@ -53681,7 +53802,7 @@ radial glial cells acting as neural progenitors throughout life. This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery. - 2010-06-30T04:23:42Z + 2010-06-30T04:23:42Z FMA:84187 sheath cell of carotid body type II cell of carotid body @@ -53719,10 +53840,10 @@ radial glial cells acting as neural progenitors throughout life. A chromaffin cell of the adrenal medulla that produces epinephrine. - 2010-07-14T09:41:42Z + 2010-07-14T09:41:42Z FMA:69322 - adremergic chromaffin cell adrenal secreting cell of the adrenal medulla + adrenergic chromaffin cell epiniphrine secreting cell of the adrenal medulla type II cell of adrenal medulla @@ -53763,7 +53884,7 @@ radial glial cells acting as neural progenitors throughout life. A chromaffin cell of the adrenal medulla that produces norepinephrine. - 2010-07-14T10:12:24Z + 2010-07-14T10:12:24Z FMA:69321 noradrenergic chromaffin cell type I cell of adrenal medulla @@ -53790,7 +53911,7 @@ radial glial cells acting as neural progenitors throughout life. A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport. - 2010-07-14T03:22:02Z + 2010-07-14T03:22:02Z Boettcher's cell Bottcher cell Bottcher's cell @@ -53812,7 +53933,7 @@ radial glial cells acting as neural progenitors throughout life. Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle. - 2010-07-15T11:21:11Z + 2010-07-15T11:21:11Z BTO:0001953 FMA:54560 stretch cell @@ -53835,7 +53956,7 @@ radial glial cells acting as neural progenitors throughout life. A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. - 2010-07-21T01:33:38Z + 2010-07-21T01:33:38Z FMA:67968 specialized cardiac myocyte @@ -53872,7 +53993,7 @@ radial glial cells acting as neural progenitors throughout life. A leukocyte that lacks granules. - 2010-07-22T11:30:33Z + 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte @@ -53917,7 +54038,7 @@ radial glial cells acting as neural progenitors throughout life. This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise. - 2010-07-22T03:26:00Z + 2010-07-22T03:26:00Z BTO:0003914 FMA:86573 ICC @@ -54131,7 +54252,7 @@ radial glial cells acting as neural progenitors throughout life. A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive. - 2010-08-12T02:22:19Z + 2010-08-12T02:22:19Z nuocyte group 2 innate lymphoid cell, mouse @@ -54152,7 +54273,7 @@ radial glial cells acting as neural progenitors throughout life. One of two small cells formed by the first and second meiotic division of oocytes. - 2010-08-23T09:49:53Z + 2010-08-23T09:49:53Z EHDAA2:0004716 FMA:85543 MESH:D059705 @@ -54177,7 +54298,7 @@ radial glial cells acting as neural progenitors throughout life. A small cell formed by the first meiotic division of oocytes. - 2010-08-23T09:49:58Z + 2010-08-23T09:49:58Z EHDAA2:0000541 EMAPA:16032 FMA:18650 @@ -54231,7 +54352,7 @@ radial glial cells acting as neural progenitors throughout life. A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. - 2010-07-22T04:48:15Z + 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 @@ -54261,7 +54382,7 @@ radial glial cells acting as neural progenitors throughout life. A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell. - 2010-08-23T09:50:01Z + 2010-08-23T09:50:01Z EHDAA2:0001820 EMAPA:16034 EMAPA:16045 @@ -54298,7 +54419,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that makes up the loose connective tissue of the ovary. - 2010-08-23T11:11:34Z + 2010-08-23T11:11:34Z FMA:18709 interstitial cell of ovary @@ -54320,7 +54441,7 @@ radial glial cells acting as neural progenitors throughout life. A cell in the hilum of the ovary that produces androgens. - 2010-08-23T11:18:18Z + 2010-08-23T11:18:18Z FMA:18710 hilar cell of ovary @@ -54360,7 +54481,7 @@ radial glial cells acting as neural progenitors throughout life. A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals. - 2010-08-23T11:24:11Z + 2010-08-23T11:24:11Z FMA:223275 internodal tract myocyte @@ -54393,7 +54514,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol. - 2010-08-24T01:37:44Z + 2010-08-24T01:37:44Z FMA:69545 adrenal cortex cell adrenocortical cell @@ -54421,7 +54542,7 @@ radial glial cells acting as neural progenitors throughout life. A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval. - 2010-08-23T11:33:10Z + 2010-08-23T11:33:10Z FMA:67967 regular cardiac muscle cell regular cardiac muscle fiber @@ -54460,7 +54581,7 @@ radial glial cells acting as neural progenitors throughout life. A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids. - 2010-08-24T01:42:02Z + 2010-08-24T01:42:02Z FMA:69273 epithelial cell of zona glomerulosa of adrenal gland type I cell of adrenal cortex @@ -54487,7 +54608,7 @@ radial glial cells acting as neural progenitors throughout life. A regular cardiac myocyte of the interventricular region of the heart. - 2010-08-23T11:40:52Z + 2010-08-23T11:40:52Z FMA:228792 regular interventricular cardiac myocyte @@ -55575,7 +55696,7 @@ radial glial cells acting as neural progenitors throughout life. A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma. - 2010-08-18T09:57:19Z + 2010-08-18T09:57:19Z gammadelta27-positive gd27-positive CD27-positive gamma-delta T cell @@ -55656,7 +55777,7 @@ radial glial cells acting as neural progenitors throughout life. A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion. - 2010-08-18T09:57:29Z + 2010-08-18T09:57:29Z gammadelta-17 cells CD27-negative gamma-delta T cell @@ -55771,7 +55892,7 @@ radial glial cells acting as neural progenitors throughout life. A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low). - 2010-08-18T10:35:37Z + 2010-08-18T10:35:37Z CD25-positive, CD27-positive immature gamma-delta T cell @@ -55813,7 +55934,7 @@ radial glial cells acting as neural progenitors throughout life. A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation. - 2010-08-20T02:14:25Z + 2010-08-20T02:14:25Z innate effector T cell @@ -55926,7 +56047,7 @@ radial glial cells acting as neural progenitors throughout life. Regular cardiac myocyte of a cardiac atrium. - 2010-08-23T11:41:03Z + 2010-08-23T11:41:03Z FMA:83108 atrial cardiac muscle cell atrial myocyte @@ -55956,7 +56077,7 @@ radial glial cells acting as neural progenitors throughout life. A cardiac myocyte of the interatrial region of the heart. - 2010-08-23T11:41:09Z + 2010-08-23T11:41:09Z FMA:228790 regular interatrial cardiac myocyte @@ -55975,7 +56096,7 @@ radial glial cells acting as neural progenitors throughout life. Regular cardiac myocyte of a cardiac ventricle. - 2010-08-23T11:41:13Z + 2010-08-23T11:41:13Z ventricular cardiac muscle cell FMA:83109 regular cardiac muscle cell of ventricle @@ -56022,7 +56143,7 @@ radial glial cells acting as neural progenitors throughout life. A stomal cell of the ovary - 2010-08-23T12:10:31Z + 2010-08-23T12:10:31Z FMA:72299 ovarian stromal cell @@ -56049,7 +56170,7 @@ radial glial cells acting as neural progenitors throughout life. A stromal cell of the ovarian cortex. - 2010-08-23T12:12:15Z + 2010-08-23T12:12:15Z FMA:256169 stromal cell of ovarian cortex @@ -56085,7 +56206,7 @@ radial glial cells acting as neural progenitors throughout life. A stromal cell of the ovarian medulla. - 2010-08-23T12:12:17Z + 2010-08-23T12:12:17Z FMA:256171 stromal cell of ovarian medulla @@ -56116,7 +56237,7 @@ radial glial cells acting as neural progenitors throughout life. Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues. - 2010-08-24T08:43:27Z + 2010-08-24T08:43:27Z FMA:62880 nonkeratinized cell of epidermis @@ -56137,7 +56258,7 @@ radial glial cells acting as neural progenitors throughout life. A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol. - 2010-08-24T01:50:42Z + 2010-08-24T01:50:42Z FMA:69547 type II cortical cell of adrenal gland type II cell of adrenal cortex @@ -56159,7 +56280,7 @@ radial glial cells acting as neural progenitors throughout life. A cell in the zona reticularis that produce sex hormones. - 2010-08-24T01:50:44Z + 2010-08-24T01:50:44Z FMA:69564 type III cell of adrenal cortex @@ -56179,15 +56300,11 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - @@ -56207,7 +56324,7 @@ radial glial cells acting as neural progenitors throughout life. A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. - 2010-08-24T02:05:28Z + 2010-08-24T02:05:28Z BTO:0004167 FMA:68458 LEC @@ -56238,7 +56355,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -56284,7 +56401,7 @@ radial glial cells acting as neural progenitors throughout life. A sebum secreting cell of the skin that secretes sebum into the hair follicles. - 2010-08-24T09:27:52Z + 2010-08-24T09:27:52Z sebocyte BTO:0004613 FMA:70953 @@ -56311,7 +56428,7 @@ radial glial cells acting as neural progenitors throughout life. A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1 - 2010-08-24T09:30:15Z + 2010-08-24T09:30:15Z FMA:69082 active chief cell of parathyroid gland @@ -56340,7 +56457,7 @@ radial glial cells acting as neural progenitors throughout life. A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus. - 2010-08-24T02:15:16Z + 2010-08-24T02:15:16Z FMA:70659 dark cell of eccrine sweat gland @@ -56359,7 +56476,7 @@ radial glial cells acting as neural progenitors throughout life. A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules. - 2010-08-24T02:18:36Z + 2010-08-24T02:18:36Z FMA:69080 dark chief cell of parathyroid gland @@ -56387,6 +56504,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56397,7 +56515,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell found in capillaries. - 2010-08-24T10:15:00Z + 2010-08-24T10:15:00Z BTO:0004956 CALOHA:TS-0112 FMA:67756 @@ -56429,7 +56547,7 @@ radial glial cells acting as neural progenitors throughout life. A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree. - 2010-08-24T03:38:29Z + 2010-08-24T03:38:29Z FMA:70542 @@ -56460,7 +56578,7 @@ radial glial cells acting as neural progenitors throughout life. A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin. - 2010-08-24T10:33:02Z + 2010-08-24T10:33:02Z FMA:70658 clear cell of eccrine sweat gland @@ -56480,7 +56598,7 @@ radial glial cells acting as neural progenitors throughout life. A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells. - 2010-08-24T10:39:42Z + 2010-08-24T10:39:42Z FMA:69081 clear chief cell of parathyroid cell clear chief cell of parathyroid gland @@ -56519,7 +56637,7 @@ radial glial cells acting as neural progenitors throughout life. A cell found within the dental pulp. - 2010-08-24T02:52:09Z + 2010-08-24T02:52:09Z CALOHA:TS-0195 FMA:87170 dental pulp cell @@ -56557,7 +56675,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the uterus. - 2010-08-24T10:45:54Z + 2010-08-24T10:45:54Z FMA:256161 epithelial cell of uterus @@ -56589,7 +56707,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation. - 2010-08-24T03:48:30Z + 2010-08-24T03:48:30Z epithelioid cell FMA:83514 epithelioid histocyte @@ -56619,7 +56737,7 @@ radial glial cells acting as neural progenitors throughout life. A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous. - 2010-08-24T03:07:50Z + 2010-08-24T03:07:50Z FMA:83534 late promyelocyte @@ -56645,7 +56763,7 @@ radial glial cells acting as neural progenitors throughout life. A columnar cell of the cervix uteri. - 2010-08-24T10:47:47Z + 2010-08-24T10:47:47Z FMA:86486 columnar cell of endocervix @@ -56680,7 +56798,7 @@ radial glial cells acting as neural progenitors throughout life. The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus. - 2010-08-24T10:53:03Z + 2010-08-24T10:53:03Z BTO:0001943 FMA:68650 @@ -56702,7 +56820,7 @@ radial glial cells acting as neural progenitors throughout life. A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages. - 2010-08-24T03:07:53Z + 2010-08-24T03:07:53Z FMA:83533 early promyelocyte @@ -56723,7 +56841,7 @@ radial glial cells acting as neural progenitors throughout life. A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease. - 2010-08-24T03:15:21Z + 2010-08-24T03:15:21Z FMA:81099 burr cell echinocyte @@ -56760,7 +56878,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones. - 2010-08-24T03:33:58Z + 2010-08-24T03:33:58Z FMA:86495 endosteal cell @@ -56781,7 +56899,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cell found on the external side of the tympanic membrane - 2010-08-25T10:25:31Z + 2010-08-25T10:25:31Z FMA:70558 external epithelial cell of tympanic membrane @@ -56801,7 +56919,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cells derived from general body ectoderm and ectoderm placodes. - 2010-08-26T08:31:08Z + 2010-08-26T08:31:08Z FMA:70556 general ecto-epithelial cell @@ -56820,7 +56938,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions. - 2010-08-25T10:28:44Z + 2010-08-25T10:28:44Z basal external epithelial cell of tympanic membrane @@ -56838,7 +56956,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus. - 2010-08-25T10:28:48Z + 2010-08-25T10:28:48Z superficial external epithelial cell of tympanic membrane @@ -56862,7 +56980,7 @@ radial glial cells acting as neural progenitors throughout life. An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones. - 2010-08-25T10:49:46Z + 2010-08-25T10:49:46Z FMA:70626 internal epithelial cell of tympanic membrane @@ -56882,7 +57000,7 @@ radial glial cells acting as neural progenitors throughout life. A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells. - 2010-08-25T11:05:21Z + 2010-08-25T11:05:21Z FMA:75726 internal pillar cell of cochlea @@ -56902,7 +57020,7 @@ radial glial cells acting as neural progenitors throughout life. A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells. - 2010-08-25T11:05:23Z + 2010-08-25T11:05:23Z FMA:75727 external pillar cell of cochlea @@ -56922,7 +57040,7 @@ radial glial cells acting as neural progenitors throughout life. A supporting cell that is attached to the basement membrane and forms rows that support the hair cells. - 2010-08-25T01:29:07Z + 2010-08-25T01:29:07Z FMA:79800 phalangeal cell @@ -56949,7 +57067,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth. - 2010-08-26T08:51:27Z + 2010-08-26T08:51:27Z FMA:62987 epithelial cell rests of Malassez epithelial debris of Malassez @@ -56997,7 +57115,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized cell involved in sensory perception of smell. - 2010-08-26T01:47:13Z + 2010-08-26T01:47:13Z FMA:67870 olfactory epithelial cell @@ -57017,7 +57135,7 @@ radial glial cells acting as neural progenitors throughout life. A border cell is a slender columnar cell on the medial portion of the basilar membrane. - 2010-08-25T01:47:12Z + 2010-08-25T01:47:12Z FMA:79798 border cell of cochlea @@ -57047,6 +57165,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -57055,7 +57174,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell located on the basal lamina of the olfactory epithelium. - 2010-08-26T01:58:54Z + 2010-08-26T01:58:54Z horizontal basal cell FMA:62303 basal cell of olfactory epithelium @@ -57101,7 +57220,7 @@ radial glial cells acting as neural progenitors throughout life. A keratinized cell located in the hard palate or gingiva. - 2010-08-26T02:51:30Z + 2010-08-26T02:51:30Z keratinized cell of the oral mucosa @@ -57120,7 +57239,7 @@ radial glial cells acting as neural progenitors throughout life. A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium. - 2010-08-26T01:59:18Z + 2010-08-26T01:59:18Z FMA:67874 blastema cell of olfactory epithelium globose cell of olfactory epithelium @@ -57147,7 +57266,7 @@ radial glial cells acting as neural progenitors throughout life. A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph. - 2010-08-25T02:02:48Z + 2010-08-25T02:02:48Z FMA:79797 interdental cell interdental cell of cochlea @@ -57188,7 +57307,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. - 2010-08-25T02:20:55Z + 2010-08-25T02:20:55Z FMA:84143 KUPO:0001033 Goormaghtigh cell @@ -57221,7 +57340,7 @@ radial glial cells acting as neural progenitors throughout life. A cell within the follicle of an ovary. - 2010-08-25T03:01:27Z + 2010-08-25T03:01:27Z EMAPA:31247 FMA:70589 follicular cell of ovary @@ -57247,7 +57366,7 @@ radial glial cells acting as neural progenitors throughout life. A cell within the primary follicle of the ovary. - 2010-08-25T03:03:42Z + 2010-08-25T03:03:42Z FMA:70590 primary follicular cell of ovary @@ -57266,7 +57385,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of a secondary follicile within the ovary. - 2010-08-25T03:03:48Z + 2010-08-25T03:03:48Z FMA:70591 secondary follicular cell of ovary @@ -57303,7 +57422,7 @@ radial glial cells acting as neural progenitors throughout life. A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature. - 2010-08-25T03:10:10Z + 2010-08-25T03:10:10Z FMA:83102 folliculostellate cell of pars anterior of adenohypophysis folliculostellate cell of pars distalis of adenohypophysis @@ -57346,7 +57465,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell found in the lining of the stomach. - 2010-08-25T03:22:08Z + 2010-08-25T03:22:08Z FMA:62948 epithelial cell of stomach @@ -57371,7 +57490,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop . - 2010-08-25T03:23:22Z + 2010-08-25T03:23:22Z FMA:86552 foveolar cell of stomach @@ -57409,7 +57528,7 @@ radial glial cells acting as neural progenitors throughout life. A mucous cell in the epithelium of the stomach. - 2010-08-25T03:38:51Z + 2010-08-25T03:38:51Z FMA:63464 mucous cell of stomach @@ -57447,7 +57566,7 @@ radial glial cells acting as neural progenitors throughout life. A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach. - 2010-08-25T03:41:30Z + 2010-08-25T03:41:30Z FMA:62954 mucus neck cell of gastric gland mucous neck cell of gastric gland @@ -57481,7 +57600,7 @@ radial glial cells acting as neural progenitors throughout life. A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. - 2010-08-25T03:45:10Z + 2010-08-25T03:45:10Z FMA:62949 surface mucosal cell of stomach @@ -57520,7 +57639,7 @@ radial glial cells acting as neural progenitors throughout life. A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. - 2010-08-25T03:57:08Z + 2010-08-25T03:57:08Z FMA:62953 stem cell of gastric gland @@ -57546,7 +57665,7 @@ radial glial cells acting as neural progenitors throughout life. A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium. - 2010-08-26T01:59:22Z + 2010-08-26T01:59:22Z FMA:62304 horizontal basal cells basal proper cell of olfactory epithelium @@ -57602,7 +57721,7 @@ radial glial cells acting as neural progenitors throughout life. A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane. - 2010-08-26T03:12:49Z + 2010-08-26T03:12:49Z FMA:70571 basal cell of epidermis @@ -57637,24 +57756,23 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. - 2010-08-26T10:59:44Z + 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 glomerular endothelial cell - - - - - true - @@ -57671,7 +57789,7 @@ radial glial cells acting as neural progenitors throughout life. A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules. - 2010-08-26T03:19:00Z + 2010-08-26T03:19:00Z FMA:70543 granular cell of epidermis @@ -57691,7 +57809,7 @@ radial glial cells acting as neural progenitors throughout life. A flat keratinocyte immediately below the cornified layer. - 2010-08-26T03:37:02Z + 2010-08-26T03:37:02Z FMA:86925 squamous cell of epidermis @@ -57728,7 +57846,7 @@ radial glial cells acting as neural progenitors throughout life. A cell involved in the formation of a granulocyte. - 2010-08-30T12:54:27Z + 2010-08-30T12:54:27Z FMA:83519 granulocytopoietic cell @@ -57761,7 +57879,7 @@ radial glial cells acting as neural progenitors throughout life. A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. - 2010-08-30T01:08:15Z + 2010-08-30T01:08:15Z FMA:83541 metamyelocyte @@ -57790,7 +57908,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. - 2010-08-30T01:08:19Z + 2010-08-30T01:08:19Z BTO:0000734 FMA:83525 @@ -57831,7 +57949,7 @@ radial glial cells acting as neural progenitors throughout life. A cell involved in the formation of a monocyte (monopoiesis). - 2010-08-30T01:27:48Z + 2010-08-30T01:27:48Z FMA:83552 monopoietic cell @@ -57873,7 +57991,7 @@ radial glial cells acting as neural progenitors throughout life. A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes). - 2010-08-30T02:00:42Z + 2010-08-30T02:00:42Z FMA:86577 HpSC hepatic stem cell @@ -57916,7 +58034,7 @@ radial glial cells acting as neural progenitors throughout life. Liver progenitor cells have been variously named in rodent and human studies as oval cells, hepatic progenitor cells, liver stem cells, ductular reactions, or atypical ductular cells. They were first described as oval cells in rats due to their large nuclear-to-cytoplasm ratio and oval-shaped nuclei. On the difference between 'hepatic liver stem cells' (HLSC) and 'oval cells': "... unlike a well-known hepatic progenitor cell population, known as oval cells in rodents, HLSCs do not express CK-7, CK-19, c-kit, CD133 and alpha-smooth muscle actin (α-SMA) (Gaudio et al., 2009)". - 2010-08-30T02:01:49Z + 2010-08-30T02:01:49Z BTO:0004270 FMA:86576 hepatic oval cell @@ -57960,7 +58078,7 @@ radial glial cells acting as neural progenitors throughout life. A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1. - 2010-09-02T11:14:01Z + 2010-09-02T11:14:01Z inactive chief cell of parathyoid gland @@ -57979,7 +58097,7 @@ radial glial cells acting as neural progenitors throughout life. A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands. - 2010-09-02T11:26:49Z + 2010-09-02T11:26:49Z FMA:67606 MESH:D024862 oxyphil @@ -58003,7 +58121,7 @@ radial glial cells acting as neural progenitors throughout life. An oncocyte located in the parathyroid gland. - 2010-09-02T11:33:23Z + 2010-09-02T11:33:23Z FMA:69084 oxyphil cell of parathyroid gland @@ -58034,7 +58152,7 @@ radial glial cells acting as neural progenitors throughout life. An oncocyte located in the thyroid. - 2010-09-02T11:33:26Z + 2010-09-02T11:33:26Z FMA:87169 Askanazy cells Hurthle cells @@ -58057,7 +58175,7 @@ radial glial cells acting as neural progenitors throughout life. A renal intercalated cell that secretes base and reabsorbs acid in the distal segments of the kidney tubule to maintain acid/base balance. - 2010-09-02T01:43:55Z + 2010-09-02T01:43:55Z type B intercalated cell type B-IC @@ -58096,7 +58214,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -58105,12 +58223,12 @@ radial glial cells acting as neural progenitors throughout life. - + An epithelial cell of the tracheobronchial tree. - 2010-09-02T02:09:14Z + 2010-09-02T02:09:14Z FMA:66816 epithelial cell of tracheobronchial tree @@ -58141,7 +58259,7 @@ radial glial cells acting as neural progenitors throughout life. Brush cell found in the epithelial layer of the colon. - 2010-09-02T02:20:50Z + 2010-09-02T02:20:50Z FMA:263222 brush cell of large intestine tuft cell of epithelium of large intestine @@ -58183,7 +58301,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. - 2010-09-02T02:28:53Z + 2010-09-02T02:28:53Z FMA:67978 caveolated cell fibrillovesicular cell @@ -58227,7 +58345,7 @@ radial glial cells acting as neural progenitors throughout life. A brush cell found in the epithelium of lobular bronchiole. - 2010-09-02T02:38:34Z + 2010-09-02T02:38:34Z FMA:263220 brush cell of lobular bronchiole @@ -58264,7 +58382,7 @@ radial glial cells acting as neural progenitors throughout life. A brush cell of the epithelium in the terminal bronchiole. - 2010-09-02T02:38:36Z + 2010-09-02T02:38:36Z FMA:263228 brush cell of terminal bronchiole @@ -58302,7 +58420,7 @@ radial glial cells acting as neural progenitors throughout life. Brush cell of the epithelium in the trachea. - 2010-09-02T02:38:37Z + 2010-09-02T02:38:37Z FMA:263224 @@ -58348,7 +58466,7 @@ radial glial cells acting as neural progenitors throughout life. A brush cell found in the epithelium of bronchus. - 2010-09-02T02:38:42Z + 2010-09-02T02:38:42Z FMA:263226 brush cell of bronchus @@ -58368,7 +58486,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells. - 2010-09-02T02:53:59Z + 2010-09-02T02:53:59Z FMA:69060 undifferentiated columnar cell of tracheobronchial tree intermediate epitheliocyte @@ -58389,7 +58507,7 @@ radial glial cells acting as neural progenitors throughout life. A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance. - 2010-09-02T03:20:03Z + 2010-09-02T03:20:03Z FMA:84448 oxidative muscle fiber red muscle fiber @@ -58412,7 +58530,7 @@ radial glial cells acting as neural progenitors throughout life. A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue. - 2010-09-02T03:24:05Z + 2010-09-02T03:24:05Z BTO:0001812 CALOHA:TS-0940 FMA:84413 @@ -58460,7 +58578,7 @@ radial glial cells acting as neural progenitors throughout life. A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate. - 2010-09-02T03:28:45Z + 2010-09-02T03:28:45Z BTO:0001813 FMA:84414 type 2 muscle cell @@ -58483,7 +58601,7 @@ radial glial cells acting as neural progenitors throughout life. A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance. - 2010-09-02T03:28:48Z + 2010-09-02T03:28:48Z FMA:84449 white muscle cell @@ -58504,7 +58622,7 @@ radial glial cells acting as neural progenitors throughout life. A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue. - 2010-09-02T03:31:38Z + 2010-09-02T03:31:38Z BTO:0001813 FMA:84415 fast twitch A @@ -58530,7 +58648,7 @@ radial glial cells acting as neural progenitors throughout life. A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity. - 2010-09-02T03:31:42Z + 2010-09-02T03:31:42Z FMA:84416 type 2b muscle cell type 2b muscle fiber @@ -58554,7 +58672,7 @@ radial glial cells acting as neural progenitors throughout life. An intermediate muscle cell that has characteristics of both fast and slow muscle cells. - 2010-09-02T03:51:17Z + 2010-09-02T03:51:17Z FMA:84450 intermediate muscle cell @@ -58573,7 +58691,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus. - 2010-09-02T04:04:36Z + 2010-09-02T04:04:36Z BTO:0002366 FMA:86564 intermediate trophoblast cell @@ -58594,7 +58712,7 @@ radial glial cells acting as neural progenitors throughout life. A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18. - 2010-10-07T01:58:00Z + 2010-10-07T01:58:00Z immature DEC precursor immature DETC precursor NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. @@ -58616,7 +58734,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua. - 2010-09-02T04:14:28Z + 2010-09-02T04:14:28Z anchoring trophoblast @@ -58635,7 +58753,7 @@ radial glial cells acting as neural progenitors throughout life. A cell located between the pinealocytes. - 2010-09-02T04:28:41Z + 2010-09-02T04:28:41Z FMA:86575 interstitial cell of pineal gland @@ -58656,7 +58774,7 @@ radial glial cells acting as neural progenitors throughout life. A squamous cell that has keratin in the esophagus. - 2010-09-07T10:11:06Z + 2010-09-07T10:11:06Z FMA:86549 keratinized squamous cell of esophagus @@ -58683,7 +58801,7 @@ radial glial cells acting as neural progenitors throughout life. A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. - 2010-09-07T10:38:03Z + 2010-09-07T10:38:03Z FMA:70950 vertebrate lens cell @@ -58704,7 +58822,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s). - 2010-09-07T10:45:45Z + 2010-09-07T10:45:45Z FMA:63181 anterior lens cell @@ -58744,7 +58862,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. - 2010-09-07T10:45:47Z + 2010-09-07T10:45:47Z FMA:67559 @@ -58781,7 +58899,7 @@ radial glial cells acting as neural progenitors throughout life. A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded. - 2010-09-07T10:53:39Z + 2010-09-07T10:53:39Z secondary lens fibre @@ -58809,7 +58927,7 @@ radial glial cells acting as neural progenitors throughout life. A secondary lens fiber cell that lacks a nucleus. - 2010-09-07T11:15:23Z + 2010-09-07T11:15:23Z FMA:67561 non-nucleated secondary lens fibre non-nucleated secondary lens fiber @@ -58829,7 +58947,7 @@ radial glial cells acting as neural progenitors throughout life. A secondary fiber cell that contains a nucleus. - 2010-09-07T11:15:26Z + 2010-09-07T11:15:26Z FMA:70949 nucleated secondary lens fibre nucleated secondary lens fiber @@ -58857,7 +58975,7 @@ radial glial cells acting as neural progenitors throughout life. An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers. - 2010-09-07T11:19:01Z + 2010-09-07T11:19:01Z FMA:70613 primary lens fibre @@ -58879,7 +58997,7 @@ radial glial cells acting as neural progenitors throughout life. A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules. - 2010-09-07T11:46:54Z + 2010-09-07T11:46:54Z FMA:69079 light chief cell of parathyroid gland @@ -58926,7 +59044,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the prostate. - 2010-09-07T01:49:29Z + 2010-09-07T01:49:29Z FMA:256163 FMA:66817 prostate epithelial cell @@ -58972,7 +59090,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of prostatic duct. - 2010-09-07T01:55:51Z + 2010-09-07T01:55:51Z FMA:74224 ductal epithelial cell of prostate epithelial cell of prostatic duct @@ -59021,7 +59139,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the prostatic acinus. - 2010-09-07T01:55:53Z + 2010-09-07T01:55:53Z FMA:74223 acinar epithelial cell of prostate epithelial cell of prostatic acinus @@ -59066,7 +59184,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the basal layer of the epithelium in the prostatic acinus. - 2010-09-07T01:59:08Z + 2010-09-07T01:59:08Z FMA:74265 basal epithelial cell of prostatic acinus basal cell of prostatic acinus @@ -59104,7 +59222,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the luminal layer of the epithelium in the prostatic acinus. - 2010-09-07T01:59:10Z + 2010-09-07T01:59:10Z FMA:74266 luminal cell of prostatic acinus @@ -59141,7 +59259,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that constitutes the basal layer of epithelium in the prostatic duct. - 2010-09-07T01:59:12Z + 2010-09-07T01:59:12Z FMA:74226 basal epithelial cell of prostatic duct @@ -59180,7 +59298,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that constitutes the luminal layer of epithelium of prostatic duct. - 2010-09-07T01:59:16Z + 2010-09-07T01:59:16Z FMA:74225 luminal epithelial cell of prostatic duct @@ -59205,7 +59323,7 @@ radial glial cells acting as neural progenitors throughout life. A primordial germ cell that is destined to become a male germ cell. - 2010-09-07T02:11:13Z + 2010-09-07T02:11:13Z EHDAA2:0001053 EMAPA:18686 FMA:84771 @@ -59241,7 +59359,7 @@ radial glial cells acting as neural progenitors throughout life. A primordial cell from which an oocyte (ovum) ultimately is developed. - 2010-09-07T02:11:16Z + 2010-09-07T02:11:16Z EHDAA2:0000505 EMAPA:17965 FMA:84772 @@ -59290,7 +59408,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast in the bone marrow. - 2010-09-07T02:25:18Z + 2010-09-07T02:25:18Z FMA:84377 marrow fibroblast @@ -59331,7 +59449,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. - 2010-09-07T02:29:38Z + 2010-09-07T02:29:38Z FMA:84467 pulmonary myofibroblast pulmonary septal cell @@ -59376,7 +59494,7 @@ radial glial cells acting as neural progenitors throughout life. A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -59418,7 +59536,7 @@ radial glial cells acting as neural progenitors throughout life. A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells. - 2010-09-08T08:53:42Z + 2010-09-08T08:53:42Z FMA:70611 smooth muscle fiber of sphincter of pupil smooth muscle fibre of sphincter of pupil @@ -59449,7 +59567,7 @@ radial glial cells acting as neural progenitors throughout life. A nonstratified squamous cell located in the ectocervix. - 2010-09-08T09:12:23Z + 2010-09-08T09:12:23Z FMA:86483 ectocervical squamous cell squamous cell of ectocervix @@ -59469,7 +59587,7 @@ radial glial cells acting as neural progenitors throughout life. OBSOLETE: A lymphocyte that lacks T or B cell surface markers. - 2010-09-07T03:43:42Z + 2010-09-07T03:43:42Z FMA:83601 obsolete null lymphocyte true @@ -59508,7 +59626,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). - 2010-09-07T03:57:09Z + 2010-09-07T03:57:09Z BTO:0002669 FMA:86711 MESH:D000072916 @@ -59536,7 +59654,7 @@ radial glial cells acting as neural progenitors throughout life. A tissue macrophage that is in the pleural space. - 2010-09-07T04:16:43Z + 2010-09-07T04:16:43Z FMA:83024 pleural macrophage @@ -59555,7 +59673,7 @@ radial glial cells acting as neural progenitors throughout life. A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta. - 2010-09-07T04:26:06Z + 2010-09-07T04:26:06Z FMA:70570 MESH:D039904 pluripotent stem cell @@ -59577,7 +59695,7 @@ radial glial cells acting as neural progenitors throughout life. A stem cell that can differentiate into a cardiac myocyte. - 2010-09-07T04:40:32Z + 2010-09-07T04:40:32Z FMA:75620 primitive cardiac myocyte @@ -59615,7 +59733,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. - 2010-09-08T09:21:22Z + 2010-09-08T09:21:22Z FMA:63379 stem cell of intestinal crypt of Lieberkuhn @@ -59654,7 +59772,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. - 2010-09-08T09:26:53Z + 2010-09-08T09:26:53Z epithelial cell of alimentary canal @@ -59690,7 +59808,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the esophagus. - 2010-09-08T09:28:20Z + 2010-09-08T09:28:20Z FMA:63071 ZFA:0009400 @@ -59740,7 +59858,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the large intestine. - 2010-09-08T09:28:22Z + 2010-09-08T09:28:22Z BTO:0004297 FMA:256157 epithelial cell of colon @@ -59785,7 +59903,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the small intestine. - 2010-09-08T09:41:46Z + 2010-09-08T09:41:46Z FMA:256159 epithelial cell of small intestine @@ -59835,7 +59953,7 @@ radial glial cells acting as neural progenitors throughout life. A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell. - 2010-09-08T09:50:04Z + 2010-09-08T09:50:04Z CALOHA:TS-1266 FMA:86490 endometrial stromal cell @@ -59875,7 +59993,7 @@ radial glial cells acting as neural progenitors throughout life. A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings. - 2010-09-08T10:34:45Z + 2010-09-08T10:34:45Z FMA:84188 carotid body sustentacular cell supporting cell of carotid body @@ -59915,7 +60033,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of thyroid gland. - 2010-09-08T01:46:51Z + 2010-09-08T01:46:51Z FMA:256167 MESH:D000072637 epithelial cell of thyroid gland @@ -59941,7 +60059,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones. - 2010-09-08T01:50:08Z + 2010-09-08T01:50:08Z BTO:0003736 CALOHA:TS-1285 FMA:68782 @@ -59967,7 +60085,7 @@ radial glial cells acting as neural progenitors throughout life. The stem cell from which glial precursor cell arises from. - 2010-09-08T02:14:14Z + 2010-09-08T02:14:14Z FMA:87171 totipotent neuroepithelial stem cell @@ -60001,7 +60119,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the parathyroid gland. - 2010-09-08T02:29:38Z + 2010-09-08T02:29:38Z FMA:70547 epithelial cell of parathyroid gland @@ -60026,7 +60144,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell found in the mucosa associated with the facial skeleton. - 2010-09-14T10:40:12Z + 2010-09-14T10:40:12Z FMA:70627 endothelial cell of viscerocranial mucosa @@ -60054,7 +60172,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -60064,7 +60182,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. - 2010-09-14T10:57:26Z + 2010-09-14T10:57:26Z FMA:63134 @@ -60086,7 +60204,7 @@ radial glial cells acting as neural progenitors throughout life. One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage. - 2010-09-08T02:33:50Z + 2010-09-08T02:33:50Z FMA:69324 transitional cell of parathyroid gland @@ -60118,7 +60236,7 @@ radial glial cells acting as neural progenitors throughout life. A type of enteroendocrine cell found in the stomach that secretes glucagon. - 2010-09-10T10:54:42Z + 2010-09-10T10:54:42Z FMA:83411 type A cell of stomach @@ -60149,7 +60267,7 @@ radial glial cells acting as neural progenitors throughout life. A D cell located in the colon. - 2010-09-10T11:37:35Z + 2010-09-10T11:37:35Z FMA:268744 colon D-cell colonic delta cell @@ -60183,7 +60301,7 @@ radial glial cells acting as neural progenitors throughout life. A type D cell of the small intestine. - 2010-09-10T01:34:22Z + 2010-09-10T01:34:22Z FMA:268736 delta cell of small intestine small intestine D-cell @@ -60217,7 +60335,7 @@ radial glial cells acting as neural progenitors throughout life. A type D cell found in the stomach. - 2010-09-10T01:36:03Z + 2010-09-10T01:36:03Z FMA:83410 delta cell of stomach stomach D-cell @@ -60240,7 +60358,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell that stores and secretes Ghrelin. - 2010-09-10T01:47:45Z + 2010-09-10T01:47:45Z FMA:63418 P/D1 enteroendocrine cell @@ -60262,7 +60380,7 @@ radial glial cells acting as neural progenitors throughout life. An endocrine cell that secretes vasoactive intestinal peptide. - 2010-09-10T01:52:20Z + 2010-09-10T01:52:20Z vasoactive intestinal peptide secreting cell @@ -60281,7 +60399,7 @@ radial glial cells acting as neural progenitors throughout life. A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine. - 2010-09-10T02:13:47Z + 2010-09-10T02:13:47Z Mo enteroendocrine cell FMA:62941 type EC2 enteroendocrine cell @@ -60304,7 +60422,7 @@ radial glial cells acting as neural progenitors throughout life. A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine. - 2010-09-10T02:13:49Z + 2010-09-10T02:13:49Z FMA:62940 type EC1 enteroendocrine cell @@ -60324,7 +60442,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect. - 2010-09-10T02:31:13Z + 2010-09-10T02:31:13Z motilin secreting cell @@ -60344,7 +60462,7 @@ radial glial cells acting as neural progenitors throughout life. A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine. - 2010-09-10T02:35:17Z + 2010-09-10T02:35:17Z FMA:63208 type ECL enteroendocrine cell @@ -60382,7 +60500,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type that secretes histamine. - 2010-09-10T03:04:42Z + 2010-09-10T03:04:42Z histamine secreting cell @@ -60423,7 +60541,7 @@ radial glial cells acting as neural progenitors throughout life. A PP cell located in the islets of the pancreas. - 2010-09-10T03:30:31Z + 2010-09-10T03:30:31Z BTO:0000805 FMA:70588 MESH:D050418 @@ -60456,7 +60574,7 @@ radial glial cells acting as neural progenitors throughout life. OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus. - 2010-09-10T03:30:33Z + 2010-09-10T03:30:33Z FMA:85400 type F cell of pancreatic acinus obsolete PP cell of pancreatic acinus @@ -60478,7 +60596,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile. - 2010-09-10T03:44:36Z + 2010-09-10T03:44:36Z FMA:62937 CCK cell @@ -60500,7 +60618,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide. - 2010-09-10T03:51:47Z + 2010-09-10T03:51:47Z FMA:62942 type K enteroendocrine cell @@ -60522,7 +60640,7 @@ radial glial cells acting as neural progenitors throughout life. A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY. - 2010-09-10T03:59:09Z + 2010-09-10T03:59:09Z FMA:62944 type L enteroendocrine cell @@ -60544,7 +60662,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell found in the ileum and jejunum that produces neurotensin. - 2010-09-10T04:08:29Z + 2010-09-10T04:08:29Z FMA:62943 N cell @@ -60567,7 +60685,7 @@ radial glial cells acting as neural progenitors throughout life. Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin. - 2010-09-10T04:44:46Z + 2010-09-10T04:44:46Z FMA:62936 type S enteroendocrine cell @@ -60588,7 +60706,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide. - 2010-09-13T09:48:34Z + 2010-09-13T09:48:34Z FMA:63421 type TG enteroendocrine cell @@ -60609,7 +60727,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the mucosa associated with facial skeleton. - 2010-09-14T11:04:02Z + 2010-09-14T11:04:02Z FMA:70581 ecto-epithelial cell of viscerocranial mucosa @@ -60630,7 +60748,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell found in the fundus and pylorus; this cell type has dense round secretory granules that contain ghrelin. - 2010-09-13T10:12:12Z + 2010-09-13T10:12:12Z FMA:63209 A-like X/A-like @@ -60653,7 +60771,7 @@ radial glial cells acting as neural progenitors throughout life. A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM. - 2010-09-13T10:57:21Z + 2010-09-13T10:57:21Z taste bud basal cell FMA:67940 type 3 taste cell @@ -60676,7 +60794,7 @@ radial glial cells acting as neural progenitors throughout life. A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities. - 2010-09-13T10:57:26Z + 2010-09-13T10:57:26Z FMA:62381 type 2 taste cell type II taste cell @@ -60698,7 +60816,7 @@ radial glial cells acting as neural progenitors throughout life. A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally. - 2010-09-13T10:57:29Z + 2010-09-13T10:57:29Z taste bud basal cell FMA:62380 type 4 taste cell @@ -60722,7 +60840,7 @@ radial glial cells acting as neural progenitors throughout life. A cell type that forms the boundary with the surrounding epithelium. - 2010-09-13T10:57:31Z + 2010-09-13T10:57:31Z FMA:67941 type V taste receptor cell @@ -60743,7 +60861,7 @@ radial glial cells acting as neural progenitors throughout life. A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST. - 2010-09-13T10:57:35Z + 2010-09-13T10:57:35Z FMA:62356 dark tongue cell type I taste cell @@ -60768,7 +60886,7 @@ radial glial cells acting as neural progenitors throughout life. A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. - 2010-09-13T11:35:24Z + 2010-09-13T11:35:24Z FMA:84058 Y bearing sperm Y-bearing sperm @@ -60790,7 +60908,7 @@ radial glial cells acting as neural progenitors throughout life. A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum. - 2010-09-13T11:35:26Z + 2010-09-13T11:35:26Z FMA:84057 X bearing sperm X-bearing sperm @@ -60813,7 +60931,7 @@ radial glial cells acting as neural progenitors throughout life. A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters. - 2010-09-13T01:40:21Z + 2010-09-13T01:40:21Z FMA:84186 glomus cell @@ -60852,7 +60970,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. - 2010-09-13T02:34:22Z + 2010-09-13T02:34:22Z CALOHA:TS-1040 FMA:72208 epithelial cell of thymus gland @@ -60884,7 +61002,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule. - 2010-09-13T02:37:23Z + 2010-09-13T02:37:23Z FMA:72209 subcapsular thymic epithelial cell type-1 epithelial cell of thymus @@ -60912,7 +61030,7 @@ radial glial cells acting as neural progenitors throughout life. A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections. - 2010-09-13T02:37:26Z + 2010-09-13T02:37:26Z FMA:72214 cystic thymic epithelial cells large mTEC @@ -60937,7 +61055,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus. - 2010-09-13T02:37:45Z + 2010-09-13T02:37:45Z FMA:72212 dark thymic epithelial cell type-4 epithelial cell of thymus @@ -60959,7 +61077,7 @@ radial glial cells acting as neural progenitors throughout life. A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex. - 2010-09-13T02:37:51Z + 2010-09-13T02:37:51Z FMA:72211 intermediate thymic epithelial cell type-3 epithelial cell of thymus @@ -60979,7 +61097,7 @@ radial glial cells acting as neural progenitors throughout life. A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla. - 2010-09-13T02:37:54Z + 2010-09-13T02:37:54Z FMA:72213 undifferentiated mTEC undifferentiated medullary thymic epithelial cell @@ -61004,7 +61122,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus. - 2010-09-13T02:37:58Z + 2010-09-13T02:37:58Z FMA:72210 pale thymic epithelial cell type-2 epithelial cell of thymus @@ -61026,7 +61144,7 @@ radial glial cells acting as neural progenitors throughout life. A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin. - 2010-09-13T03:23:25Z + 2010-09-13T03:23:25Z spindle shaped mTEC spindle shaped medullary thymic epithelial cell type-7 epithelial cell of thymus @@ -61077,7 +61195,7 @@ radial glial cells acting as neural progenitors throughout life. A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles. - 2010-09-13T03:39:14Z + 2010-09-13T03:39:14Z BTO:0003652 FMA:66788 fibroblast-like synoviocyte @@ -61122,23 +61240,23 @@ radial glial cells acting as neural progenitors throughout life. - + A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. - 2010-09-13T03:39:17Z + 2010-09-13T03:39:17Z FMA:66787 type A synoviocyte Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell - + - + PMID:10770586 @@ -61170,7 +61288,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. - 2010-09-13T04:09:27Z + 2010-09-13T04:09:27Z FMA:70606 PE cell @@ -61213,7 +61331,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of non-pigmented ciliary epithelium. This cell type participates in aqueous humor formation by releasing solute, principally sodium and chloride ions received from pigmented epithelial cells via gap junctions, into the aqueous humor of the eye. - 2010-09-13T04:09:31Z + 2010-09-13T04:09:31Z FMA:70607 NPE cell nonpigmented ciliary epithelial cell @@ -61311,7 +61429,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -61329,6 +61446,7 @@ radial glial cells acting as neural progenitors throughout life. + The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. epithelial cell of proximal tubule @@ -61350,18 +61468,32 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + - A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow. + A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste. - 2010-09-14T11:29:20Z + 2010-09-14T11:29:20Z + The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. brush border cell of the proximal tubule - A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow. + A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste. GOC:tfm ISBN:1-4160-2328-3 + PMID:23799132 @@ -61389,7 +61521,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of a skin gland. - 2010-09-14T12:00:07Z + 2010-09-14T12:00:07Z FMA:70657 epithelial cell of gland of skin epithelial cell of skin gland @@ -61410,7 +61542,7 @@ radial glial cells acting as neural progenitors throughout life. A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells; - 2010-09-14T02:08:23Z + 2010-09-14T02:08:23Z BTO:0002509 FMA:83098 MESH:D052680 @@ -61434,7 +61566,7 @@ radial glial cells acting as neural progenitors throughout life. An acidophil cell of the anterior pituitary gland that produces both prolactin and growth hormone. - 2010-09-14T02:25:34Z + 2010-09-14T02:25:34Z FMA:83097 mammosomatotroph @@ -61454,7 +61586,7 @@ radial glial cells acting as neural progenitors throughout life. An acidophilic cell of the anterior pituitary that produces prolactin. - 2010-09-14T02:30:57Z + 2010-09-14T02:30:57Z FMA:83096 epsilon-acidophil lactotrope @@ -61481,7 +61613,7 @@ radial glial cells acting as neural progenitors throughout life. An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin. - 2010-09-14T02:33:09Z + 2010-09-14T02:33:09Z FMA:83095 MESH:D052683 somatotrope @@ -61532,7 +61664,7 @@ radial glial cells acting as neural progenitors throughout life. An ecto-epithelial cell of the prostate gland that secretes hormones. - 2010-09-14T03:01:58Z + 2010-09-14T03:01:58Z CALOHA:TS-1280 FMA:74390 FMA:86774 @@ -61555,7 +61687,7 @@ radial glial cells acting as neural progenitors throughout life. An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein. - 2010-09-14T03:20:01Z + 2010-09-14T03:20:01Z FMA:75809 external supporting cell of vestibular epithelium @@ -61593,7 +61725,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial supporting cell located in the cochlea. - 2010-09-14T03:31:38Z + 2010-09-14T03:31:38Z FMA:79796 supporting cell of cochlea @@ -61629,7 +61761,7 @@ radial glial cells acting as neural progenitors throughout life. A supporting cell of the vestibular epithelium. - 2010-09-14T03:31:44Z + 2010-09-14T03:31:44Z FMA:75607 supporting cell of vestibular epithelium @@ -61649,7 +61781,7 @@ radial glial cells acting as neural progenitors throughout life. An external limiting cell found in the vestibular epithelium. - 2010-09-14T03:33:50Z + 2010-09-14T03:33:50Z FMA:75808 external limiting cell of vestibular epithelium @@ -61675,7 +61807,7 @@ radial glial cells acting as neural progenitors throughout life. A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium. - 2010-09-15T10:47:11Z + 2010-09-15T10:47:11Z FMA:86712 peripheral blood mesothelial cell @@ -61712,7 +61844,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -61751,7 +61883,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -61781,7 +61913,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -61810,7 +61942,7 @@ radial glial cells acting as neural progenitors throughout life. A stem cell of embryonic origin. - 2010-09-15T03:44:35Z + 2010-09-15T03:44:35Z BTO:0001086 CALOHA:TS-0263 FMA:82841 @@ -61855,7 +61987,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. - 2010-09-20T10:13:37Z + 2010-09-20T10:13:37Z BTO:0000066 amniocyte @@ -61896,7 +62028,7 @@ radial glial cells acting as neural progenitors throughout life. - 2010-09-20T11:42:14Z + 2010-09-20T11:42:14Z basal myoepithelial cell basal-myoepithelial cell CALOHA:TS-2378 @@ -62006,7 +62138,7 @@ radial glial cells acting as neural progenitors throughout life. - 2010-09-20T01:30:57Z + 2010-09-20T01:30:57Z mammary alveolar cell FMA:74506 FMA:79866 @@ -62079,7 +62211,7 @@ radial glial cells acting as neural progenitors throughout life. A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast. - 2010-09-20T01:37:53Z + 2010-09-20T01:37:53Z mature luminal cell FMA:73280 @@ -62124,7 +62256,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the mammary gland. - 2010-09-20T01:49:37Z + 2010-09-20T01:49:37Z BTO:0004300 breast epithelial cell mammary epithelial cell @@ -62164,7 +62296,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the bronchus. - 2010-09-20T02:00:00Z + 2010-09-20T02:00:00Z BTO:0002922 bronchial epithelial cell @@ -62185,7 +62317,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. - 2010-09-20T02:10:36Z + 2010-09-20T02:10:36Z basal epithelial cell of tracheobronchial tree @@ -62205,7 +62337,7 @@ radial glial cells acting as neural progenitors throughout life. An undifferentiated columnar cell of the bronchus epithelium - 2010-09-20T02:17:58Z + 2010-09-20T02:17:58Z undifferentiated cell of bronchus epithelium @@ -62247,7 +62379,7 @@ radial glial cells acting as neural progenitors throughout life. A ciliated cell of the bronchus. - 2010-09-20T02:21:12Z + 2010-09-20T02:21:12Z ciliated cell of the bronchus @@ -62285,7 +62417,7 @@ radial glial cells acting as neural progenitors throughout life. An adipocyte derived from a neural crest cell. - 2010-09-20T02:25:25Z + 2010-09-20T02:25:25Z neural crest derived adipocyte @@ -62304,7 +62436,7 @@ radial glial cells acting as neural progenitors throughout life. An undifferentiated fibroblast that can be stimulated to form a fat cell. - 2010-09-20T02:31:53Z + 2010-09-20T02:31:53Z BTO:0001107 preadipocyte @@ -62324,7 +62456,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha). - 2010-09-20T02:38:38Z + 2010-09-20T02:38:38Z brown preadipocyte @@ -62343,7 +62475,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek. - 2010-09-20T02:52:54Z + 2010-09-20T02:52:54Z buccal mucosa cell @@ -62365,7 +62497,7 @@ radial glial cells acting as neural progenitors throughout life. A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair. - 2010-09-20T03:07:03Z + 2010-09-20T03:07:03Z bulge keratinocyte @@ -62459,7 +62591,7 @@ radial glial cells acting as neural progenitors throughout life. A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive. - 2010-09-21T10:06:53Z + 2010-09-21T10:06:53Z p-NK Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). @@ -62501,7 +62633,7 @@ radial glial cells acting as neural progenitors throughout life. A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium. - 2010-09-20T03:21:06Z + 2010-09-20T03:21:06Z CD133-positive prostate epithelial cell prostate stem cell @@ -62522,7 +62654,7 @@ radial glial cells acting as neural progenitors throughout life. The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival. - 2010-09-20T03:34:05Z + 2010-09-20T03:34:05Z luminal cell of prostate epithelium @@ -62543,7 +62675,7 @@ radial glial cells acting as neural progenitors throughout life. An undifferentiated cell of the prostate epithelium that lacks secretory activity. - 2010-09-20T03:34:10Z + 2010-09-20T03:34:10Z basal cell of prostate epithelium @@ -62564,7 +62696,7 @@ radial glial cells acting as neural progenitors throughout life. A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage. - 2010-09-20T03:49:58Z + 2010-09-20T03:49:58Z circulating endothelial cell @@ -62631,7 +62763,7 @@ radial glial cells acting as neural progenitors throughout life. A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy. - 2010-09-20T04:00:02Z + 2010-09-20T04:00:02Z dNK cell decidual NK cell @@ -62721,7 +62853,7 @@ radial glial cells acting as neural progenitors throughout life. A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive. - 2010-09-20T04:33:11Z + 2010-09-20T04:33:11Z p-NK Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). CD56-negative, CD161-positive immature natural killer cell, human @@ -62823,7 +62955,7 @@ radial glial cells acting as neural progenitors throughout life. An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver. - 2010-09-20T04:41:01Z + 2010-09-20T04:41:01Z preNK.BM Markers are associated with mouse cells. CD27-low, CD11b-low immature natural killer cell, mouse @@ -62882,7 +63014,7 @@ radial glial cells acting as neural progenitors throughout life. An immature natural killer cell that is NK1.1-positive and DX-5 negative. - 2010-09-21T10:11:44Z + 2010-09-21T10:11:44Z Dx5-negative, NK1.1-positive immature natural killer cell, mouse @@ -62948,7 +63080,7 @@ radial glial cells acting as neural progenitors throughout life. A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion. - 2010-09-21T10:19:49Z + 2010-09-21T10:19:49Z CD27-high, CD11b-high natural killer cell, mouse @@ -63010,7 +63142,7 @@ radial glial cells acting as neural progenitors throughout life. A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors. - 2010-09-21T10:19:54Z + 2010-09-21T10:19:54Z CD27-low, CD11b-high natural killer cell, mouse @@ -63072,7 +63204,7 @@ radial glial cells acting as neural progenitors throughout life. A natural killer cell that is CD27-high and CD11b-low. - 2010-09-21T10:20:00Z + 2010-09-21T10:20:00Z CD27-high, CD11b-low natural killer cell, mouse @@ -63109,7 +63241,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. - 2010-09-21T04:33:05Z + 2010-09-21T04:33:05Z FMA:75621 endocardial endothelial cell endothelial cell of endocardium @@ -63139,7 +63271,7 @@ radial glial cells acting as neural progenitors throughout life. A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1. - 2010-09-21T04:41:06Z + 2010-09-21T04:41:06Z pancreatic endocrine progenitor pancreatic islet progenitor cell @@ -63180,7 +63312,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem cell that exists during embryogenesis. - 2010-09-22T09:05:13Z + 2010-09-22T09:05:13Z gestational hematopoietic stem cell @@ -63292,7 +63424,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. - 2010-09-22T09:08:32Z + 2010-09-22T09:08:32Z fetal liver hematopoietic progenitor cell @@ -63391,7 +63523,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive. - 2010-09-22T09:08:34Z + 2010-09-22T09:08:34Z hemangioblast precursor yolk sac hematopoietic stem cell @@ -63470,7 +63602,7 @@ radial glial cells acting as neural progenitors throughout life. A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation. - 2010-09-22T09:27:05Z + 2010-09-22T09:27:05Z primitive erythroblast primitive erythrocyte primitive erythroid cell @@ -63527,7 +63659,7 @@ radial glial cells acting as neural progenitors throughout life. A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains. - 2010-09-22T09:35:16Z + 2010-09-22T09:35:16Z megalocyte primitive reticulocyte @@ -63587,7 +63719,7 @@ radial glial cells acting as neural progenitors throughout life. A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins. - 2010-09-22T09:38:32Z + 2010-09-22T09:38:32Z macrocyte fetal derived definitive erythrocyte @@ -63640,7 +63772,7 @@ radial glial cells acting as neural progenitors throughout life. Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte. - 2010-09-22T10:02:37Z + 2010-09-22T10:02:37Z pyrenocyte @@ -63681,7 +63813,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. - 2010-09-22T10:30:02Z + 2010-09-22T10:30:02Z placental hematopoietic stem cell @@ -63700,7 +63832,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC. - 2010-09-22T10:31:49Z + 2010-09-22T10:31:49Z AGM hematopoietic stem cell @@ -63742,7 +63874,7 @@ radial glial cells acting as neural progenitors throughout life. A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41. - 2010-09-22T10:47:28Z + 2010-09-22T10:47:28Z EryP-CFC inner blood island hemangioblast primitive erythroid progenitor @@ -63777,7 +63909,7 @@ radial glial cells acting as neural progenitors throughout life. A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and HNK1-positive. - 2010-09-22T01:40:44Z + 2010-09-22T01:40:44Z granule cell precursor granule cell progenitor GCP @@ -63836,7 +63968,7 @@ radial glial cells acting as neural progenitors throughout life. A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. - 2010-09-22T01:57:40Z + 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte @@ -63878,7 +64010,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. - 2010-09-23T03:17:12Z + 2010-09-23T03:17:12Z BTO:0004562 cTEC @@ -63918,7 +64050,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. - 2010-09-23T03:17:14Z + 2010-09-23T03:17:14Z BTO:0004563 mTEC @@ -63957,7 +64089,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin. - 2010-09-23T03:46:34Z + 2010-09-23T03:46:34Z BTO:0004519 myometrium smooth muscle cell @@ -63996,7 +64128,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure. - 2010-09-23T04:18:50Z + 2010-09-23T04:18:50Z trabeculocyte trabecular meshwork cell @@ -64022,10 +64154,10 @@ radial glial cells acting as neural progenitors throughout life. - + - + @@ -64034,23 +64166,17 @@ radial glial cells acting as neural progenitors throughout life. - + An endo-epithelial cell of the respiratory tract. - 2010-09-23T04:38:49Z + 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell respiratory epithelial cell - - - - - true - @@ -64066,7 +64192,7 @@ radial glial cells acting as neural progenitors throughout life. A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions. - 2010-10-01T09:02:42Z + 2010-10-01T09:02:42Z MESH:D013172 fungal spore @@ -64089,21 +64215,16 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - + A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. - 2010-09-23T04:42:27Z + 2010-09-23T04:42:27Z respiratory mucosa goblet cells respiratory goblet cell @@ -64131,7 +64252,7 @@ radial glial cells acting as neural progenitors throughout life. - 2010-09-24T09:44:42Z + 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 @@ -64182,7 +64303,7 @@ radial glial cells acting as neural progenitors throughout life. A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. - 2010-09-24T01:13:01Z + 2010-09-24T01:13:01Z FBbt:00005812 myotubule single cell sarcomere @@ -64212,7 +64333,7 @@ radial glial cells acting as neural progenitors throughout life. A peptide hormone secreting cell that secretes growth hormone releasing hormone. - 2010-09-24T01:36:44Z + 2010-09-24T01:36:44Z GHRH secreting cell somatocrinin secreting cell growth hormone releasing hormone secreting cell @@ -64251,7 +64372,7 @@ radial glial cells acting as neural progenitors throughout life. A hair cell of the ear that contains the organs of balance and hearing. - 2010-09-24T01:49:31Z + 2010-09-24T01:49:31Z ear receptor cell ear hair cell @@ -64277,9 +64398,9 @@ radial glial cells acting as neural progenitors throughout life. - A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. + A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. - 2010-09-24T02:06:10Z + 2010-09-24T02:06:10Z Schwann cell precursor cell Schwann cell precursor @@ -64287,7 +64408,7 @@ radial glial cells acting as neural progenitors throughout life. - A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. + A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. GOC:tfm @@ -64305,7 +64426,7 @@ radial glial cells acting as neural progenitors throughout life. A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells. - 2010-09-24T02:10:26Z + 2010-09-24T02:10:26Z Schwann cell non-myelinating Schwann cell @@ -64332,7 +64453,7 @@ radial glial cells acting as neural progenitors throughout life. A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons. - 2010-09-24T02:10:31Z + 2010-09-24T02:10:31Z Schwann cell ZFA:0001725 @@ -64361,7 +64482,7 @@ radial glial cells acting as neural progenitors throughout life. A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive and is found in the fetal thymus. - 2010-10-07T02:21:07Z + 2010-10-07T02:21:07Z fetal Vgamma2+ thymocyte NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature Vgamma2-positive fetal thymocyte @@ -64382,7 +64503,7 @@ radial glial cells acting as neural progenitors throughout life. A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood. - 2010-09-28T02:23:46Z + 2010-09-28T02:23:46Z FMA:86588 arachnoid cap cell meningothelial cell @@ -64403,7 +64524,7 @@ radial glial cells acting as neural progenitors throughout life. An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere. - 2010-10-01T09:22:45Z + 2010-10-01T09:22:45Z FAO:0000039 oospore @@ -64424,7 +64545,7 @@ radial glial cells acting as neural progenitors throughout life. A conidium that has only one nucleus. - 2010-10-01T09:26:39Z + 2010-10-01T09:26:39Z FAO:0000025 uninucleate conidium @@ -64444,7 +64565,7 @@ radial glial cells acting as neural progenitors throughout life. A conidium that has more than one nucleus. - 2010-10-01T09:31:28Z + 2010-10-01T09:31:28Z FAO:0000033 multinucleate conidium @@ -64719,7 +64840,7 @@ radial glial cells acting as neural progenitors throughout life. A monocyte that has characteristics of both patrolling and inflammatory monocytes. - 2010-10-04T10:52:03Z + 2010-10-04T10:52:03Z intermediate monocyte @@ -64783,7 +64904,7 @@ radial glial cells acting as neural progenitors throughout life. A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta. - 2010-10-04T02:38:58Z + 2010-10-04T02:38:58Z Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs. @@ -64871,7 +64992,7 @@ radial glial cells acting as neural progenitors throughout life. A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative. - 2010-10-04T11:26:18Z + 2010-10-04T11:26:18Z Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Gr1-high classical monocyte @@ -64934,7 +65055,7 @@ radial glial cells acting as neural progenitors throughout life. A patrolling monocyte that is CD14-low and CD16-positive. - 2010-10-04T12:25:42Z + 2010-10-04T12:25:42Z non-classical monocyte, human @@ -64990,7 +65111,7 @@ radial glial cells acting as neural progenitors throughout life. A CD14-positive monocyte that is also CD16-positive and CCR2-negative. - 2010-10-04T12:49:47Z + 2010-10-04T12:49:47Z CD16+ monocyte This cell type is compatible with the HIPC Lyoplate markers for 'CD16+ monocyte'. Markers are associated with human cells. Note that this cell type encompasses both human intermediate monocytes (CD14+, CD16-low), and human non-classical monocytes (CD14-low, CD16+). @@ -65062,7 +65183,7 @@ radial glial cells acting as neural progenitors throughout life. An intermediate monocyte that is Gr1-positive, CD43-positive. - 2010-10-04T12:49:49Z + 2010-10-04T12:49:49Z Gr1-positive, CD43-positive monocyte @@ -65109,7 +65230,7 @@ radial glial cells acting as neural progenitors throughout life. A myeloid dendritic cell found in the blood that is CD1c-positive. - 2010-10-04T02:39:01Z + 2010-10-04T02:39:01Z Normally represent 10-20% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10) [PMID:20204387]. Upon TLR stimulation, these cells were potent producers of CXCL8 (IL-8), while producing little TNF-alpha. @@ -65184,7 +65305,7 @@ radial glial cells acting as neural progenitors throughout life. A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive. - 2010-10-05T10:11:38Z + 2010-10-05T10:11:38Z fraction B/C precursor B cell @@ -65215,7 +65336,7 @@ radial glial cells acting as neural progenitors throughout life. A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18. - 2010-10-07T02:05:46Z + 2010-10-07T02:05:46Z mature DEC precursor mature DETC precursor NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. @@ -65307,7 +65428,7 @@ radial glial cells acting as neural progenitors throughout life. A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative. - 2010-10-05T11:18:03Z + 2010-10-05T11:18:03Z Peyers patch B cell Peyer's patch B cell @@ -65333,7 +65454,7 @@ radial glial cells acting as neural progenitors throughout life. A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus. - 2010-10-07T02:24:36Z + 2010-10-07T02:24:36Z fetal Vgamma2-positive NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature Vgamma2-positive fetal thymocyte @@ -65354,7 +65475,7 @@ radial glial cells acting as neural progenitors throughout life. A thymocyte found in the fetal thymus. - 2010-10-07T02:28:25Z + 2010-10-07T02:28:25Z fetal thymocyte @@ -65392,7 +65513,7 @@ radial glial cells acting as neural progenitors throughout life. A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative). - 2010-10-07T02:33:39Z + 2010-10-07T02:33:39Z gammadelta thymocyte gd thymocyte gamma-delta thymocyte @@ -65413,7 +65534,7 @@ radial glial cells acting as neural progenitors throughout life. A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. - 2010-10-07T02:53:44Z + 2010-10-07T02:53:44Z Vgamma2-positive thymocyte NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature Vgamma2-positive thymocyte @@ -65440,7 +65561,7 @@ radial glial cells acting as neural progenitors throughout life. A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. - 2010-10-07T02:53:48Z + 2010-10-07T02:53:48Z Vgamma2-positive NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature Vgamma2-positive thymocyte @@ -65461,7 +65582,7 @@ radial glial cells acting as neural progenitors throughout life. A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain that does not contain a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. - 2010-10-07T02:59:05Z + 2010-10-07T02:59:05Z Vgamma2-negative thymocyte NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. immature Vgamma2-negative thymocyte @@ -65488,7 +65609,7 @@ radial glial cells acting as neural progenitors throughout life. A thymocyte that has a T cell receptor consisting of a gamma chain that does not contain the Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. - 2010-10-07T02:59:08Z + 2010-10-07T02:59:08Z Vgamma2-negative NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. mature Vgamma2-negative thymocyte @@ -65516,7 +65637,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast. - 2010-11-10T09:40:33Z + 2010-11-10T09:40:33Z MESH:D058954 PaSC pancreas stellate cell @@ -65541,7 +65662,7 @@ radial glial cells acting as neural progenitors throughout life. A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor. - 2010-10-07T03:07:44Z + 2010-10-07T03:07:44Z Vg1.1-positive, Vd6.3-negative T cell Vgamma1.1-positive, Vdelta6.3-negative thymocyte @@ -65561,7 +65682,7 @@ radial glial cells acting as neural progenitors throughout life. A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor. - 2010-10-07T03:03:00Z + 2010-10-07T03:03:00Z Vg1.1+Vd6.3+ T cell Vgamma1.1-positive, Vdelta6.3-positive thymocyte @@ -65581,7 +65702,7 @@ radial glial cells acting as neural progenitors throughout life. A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative. - 2010-10-07T03:10:32Z + 2010-10-07T03:10:32Z mature Vg1.1-positive, Vd6.3-negative T cell mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte @@ -65601,7 +65722,7 @@ radial glial cells acting as neural progenitors throughout life. A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive. - 2010-10-07T03:10:35Z + 2010-10-07T03:10:35Z immature Vg1.1-positive, Vd6.3-negative T cell immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte @@ -65621,7 +65742,7 @@ radial glial cells acting as neural progenitors throughout life. A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive. - 2010-10-07T03:10:39Z + 2010-10-07T03:10:39Z immature Vg1.1+Vd6.3+ T cell immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte @@ -65641,7 +65762,7 @@ radial glial cells acting as neural progenitors throughout life. A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative. - 2010-10-07T03:10:41Z + 2010-10-07T03:10:41Z mature Vg1.1+Vd6.3+ T cell mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte @@ -65661,7 +65782,7 @@ radial glial cells acting as neural progenitors throughout life. An immature or mature cell of the first erythroid lineage to arise during embryonic development. - 2010-10-12T11:22:41Z + 2010-10-12T11:22:41Z primitive erythroid lineage cell @@ -65686,7 +65807,7 @@ radial glial cells acting as neural progenitors throughout life. A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells. - 2010-10-12T12:21:16Z + 2010-10-12T12:21:16Z MESH:D055018 hemangioblast @@ -65734,7 +65855,7 @@ radial glial cells acting as neural progenitors throughout life. A T cell that expresses a T cell receptor complex and has completed T cell selection. - 2010-10-12T01:56:15Z + 2010-10-12T01:56:15Z CD3e-positive T cell mature T-cell CD3epsilon T cell @@ -65779,7 +65900,7 @@ radial glial cells acting as neural progenitors throughout life. A T cell that has not completed T cell selection. - 2010-10-12T01:56:17Z + 2010-10-12T01:56:17Z BTO:0001372 CALOHA:TS-1042 immature T-cell @@ -65820,7 +65941,7 @@ radial glial cells acting as neural progenitors throughout life. A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. - 2010-10-15T09:24:05Z + 2010-10-15T09:24:05Z nucleated reticulocyte @@ -65869,7 +65990,7 @@ radial glial cells acting as neural progenitors throughout life. A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. - 2010-10-15T09:24:08Z + 2010-10-15T09:24:08Z CALOHA:TS-0864 FMA:66785 @@ -65915,7 +66036,7 @@ radial glial cells acting as neural progenitors throughout life. A DN2 thymocyte that is Kit-hi. - 2010-10-21T10:12:05Z + 2010-10-21T10:12:05Z Observed in mice. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. DN2a thymocyte @@ -65964,7 +66085,7 @@ radial glial cells acting as neural progenitors throughout life. A DN2 thymocyte that is Kit-low. - 2010-10-21T10:12:08Z + 2010-10-21T10:12:08Z Observed in mice. There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in mouse versus human thymus. If in doubt, please consider using CL:0002489 'double negative thymocyte'. DN2b thymocyte @@ -66038,7 +66159,7 @@ radial glial cells acting as neural progenitors throughout life. A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive. - 2010-10-21T01:16:24Z + 2010-10-21T01:16:24Z ETP preT.ETP.Th @@ -66101,7 +66222,7 @@ radial glial cells acting as neural progenitors throughout life. A mature natural killer cell that is CD11b-positive and CD27-positive. - 2010-10-25T03:07:59Z + 2010-10-25T03:07:59Z A natural killer cell that is NK1.1-positive, CD11b-positive, and CD27-positive. CD11b-positive, CD27-positive natural killer cell, mouse @@ -66138,7 +66259,7 @@ radial glial cells acting as neural progenitors throughout life. A double-positive, alpha-beta thymocyte that is small and not proliferating. - 2010-10-21T01:59:06Z + 2010-10-21T01:59:06Z T.DP.sm.Th resting double-positive thymocyte @@ -66197,7 +66318,7 @@ radial glial cells acting as neural progenitors throughout life. A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating. - 2010-10-21T01:59:11Z + 2010-10-21T01:59:11Z T.DPb.Th activated double-positive thymocyte double-positive blast @@ -66267,7 +66388,7 @@ radial glial cells acting as neural progenitors throughout life. A double-positive thymocyte that is CD69-positive and has begun positive selection. - 2010-10-21T02:11:52Z + 2010-10-21T02:11:52Z T.DP69+.Th CD69-positive double-positive thymocyte @@ -66346,7 +66467,7 @@ radial glial cells acting as neural progenitors throughout life. A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor. - 2010-10-21T02:29:19Z + 2010-10-21T02:29:19Z T.4int8+.Th T_4int8+_Th CD4-intermediate, CD8-positive double-positive thymocyte @@ -66426,7 +66547,7 @@ radial glial cells acting as neural progenitors throughout life. A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor. - 2010-10-21T02:29:23Z + 2010-10-21T02:29:23Z T.4+8int.Th T_4+8int_Th CD4-positive, CD8-intermediate double-positive thymocyte @@ -66486,7 +66607,7 @@ radial glial cells acting as neural progenitors throughout life. A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. - 2010-10-21T02:43:52Z + 2010-10-21T02:43:52Z CD24-positive, CD4 single-positive semimature thymocyte T.4SP24int.Th Described in the immgene database as being CD24-intermediate. @@ -66547,7 +66668,7 @@ radial glial cells acting as neural progenitors throughout life. A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. - 2010-10-21T02:46:02Z + 2010-10-21T02:46:02Z T.4SP69+.Th intermediate CD4-single-positive CD69-positive, CD4-positive single-positive thymocyte @@ -66607,7 +66728,7 @@ radial glial cells acting as neural progenitors throughout life. A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. - 2010-10-21T02:59:10Z + 2010-10-21T02:59:10Z CD24-positive, CD8 single-positive semimature thymocyte T.8SP24int.Th Described in the immgene database as being CD24-intermediate. @@ -66668,7 +66789,7 @@ radial glial cells acting as neural progenitors throughout life. A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. - 2010-10-21T02:59:14Z + 2010-10-21T02:59:14Z T.8SP69+.Th intermediate CD8-single-positive CD69-positive, CD8-positive single-positive thymocyte @@ -66730,7 +66851,7 @@ radial glial cells acting as neural progenitors throughout life. A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. - 2010-10-21T03:31:19Z + 2010-10-21T03:31:19Z T.4SP24-.Th mature CD4 single-positive thymocyte @@ -66797,7 +66918,7 @@ radial glial cells acting as neural progenitors throughout life. A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. - 2010-10-21T03:51:50Z + 2010-10-21T03:51:50Z T.8SP24-.Th mature CD8 single-positive thymocyte @@ -66851,7 +66972,7 @@ radial glial cells acting as neural progenitors throughout life. A mature NK cell that is NK1.1-positive. - 2010-10-25T03:18:04Z + 2010-10-25T03:18:04Z NK.sp NK1.1-positive NK cell Note: Nk1.1 expression is restricted to C57BL strains of laboratory mice. @@ -66893,7 +67014,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is NKGA2-positive. - 2010-10-25T03:31:09Z + 2010-10-25T03:31:09Z NK.G2A+.SP NKGA2-positive natural killer cell, mouse @@ -66934,7 +67055,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is Ly49D-positive. - 2010-10-25T03:36:19Z + 2010-10-25T03:36:19Z NK.49D+.Sp Ly49D-positive natural killer cell, mouse @@ -66975,7 +67096,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is CD94-positive. - 2010-10-25T03:36:28Z + 2010-10-25T03:36:28Z NK.94+.Sp CD94-positive natural killer cell, mouse @@ -67032,7 +67153,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative. - 2010-10-25T03:56:21Z + 2010-10-25T03:56:21Z CD94- Ly49I-negative NK cell NK.49Cl-94-.Sp CD94-negative, Ly49CI-negative natural killer cell, mouse @@ -67074,7 +67195,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is Ly49Cl-positive. - 2010-10-25T03:36:38Z + 2010-10-25T03:36:38Z Ly49I-positive NK cell NK.49Cl+.Sp Ly49CI-positive natural killer cell, mouse @@ -67116,7 +67237,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is Ly49H-positive. - 2010-10-25T03:36:43Z + 2010-10-25T03:36:43Z LyH49H-positive Ly49H-positive natural killer cell, mouse @@ -67157,7 +67278,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is Ly49D-negative. - 2010-10-25T03:39:02Z + 2010-10-25T03:39:02Z NK.49D-.Sp Ly49D-negative natural killer cell, mouse @@ -67198,7 +67319,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is Ly49Cl-negative. - 2010-10-25T03:52:04Z + 2010-10-25T03:52:04Z Ly49I-negative NK cell NK.49Cl-.Sp Ly49CI-negative natural killer cell, mouse @@ -67240,7 +67361,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is CD94-negative. - 2010-10-25T03:54:18Z + 2010-10-25T03:54:18Z NK.94-.Sp CD94-negative natural killer cell, mouse @@ -67281,7 +67402,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is Ly49H-negative. - 2010-10-25T03:42:42Z + 2010-10-25T03:42:42Z LyH49H-negative Ly49H-negative natural killer cell, mouse @@ -67321,7 +67442,7 @@ radial glial cells acting as neural progenitors throughout life. A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive. - 2010-10-25T03:56:27Z + 2010-10-25T03:56:27Z NK.49Cl+94+.Sp CD94-positive Ly49CI-positive natural killer cell, mouse @@ -67341,7 +67462,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place. - 2010-11-10T01:41:00Z + 2010-11-10T01:41:00Z ZFA:0005565 tether cell @@ -67368,7 +67489,7 @@ radial glial cells acting as neural progenitors throughout life. A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi. - 2010-11-10T01:46:51Z + 2010-11-10T01:46:51Z mammary stem cell @@ -67418,7 +67539,7 @@ radial glial cells acting as neural progenitors throughout life. A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. - 2010-11-10T02:51:34Z + 2010-11-10T02:51:34Z oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell oligodendrocyte/type-2 astrocyte progenitor cell MESH:D000073637 @@ -67512,7 +67633,7 @@ radial glial cells acting as neural progenitors throughout life. Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. - 2010-11-22T01:10:28Z + 2010-11-22T01:10:28Z DC.8-4-11b+ spleen double-negative dendritic cell Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell @@ -67566,7 +67687,7 @@ radial glial cells acting as neural progenitors throughout life. A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive. - 2010-11-22T01:27:37Z + 2010-11-22T01:27:37Z DC.pDC.8- CD8_alpha-negative plasmacytoid dendritic cell @@ -67619,7 +67740,7 @@ radial glial cells acting as neural progenitors throughout life. A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive. - 2010-11-22T01:23:07Z + 2010-11-22T01:23:07Z DC.pDC.8+ CD8_alpha-positive plasmacytoid dendritic cell @@ -67688,7 +67809,7 @@ radial glial cells acting as neural progenitors throughout life. A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive. - 2010-11-22T03:57:57Z + 2010-11-22T03:57:57Z epidermal Langerhans cell @@ -67727,7 +67848,7 @@ radial glial cells acting as neural progenitors throughout life. A dermal dendritic cell that is langerin-positive and CD103-positive. - 2010-11-22T04:06:22Z + 2010-11-22T04:06:22Z langerin-positive dermal dendritic cell @@ -67773,7 +67894,7 @@ radial glial cells acting as neural progenitors throughout life. A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive. - 2010-11-22T04:09:44Z + 2010-11-22T04:09:44Z langerin-negative dermal dendritic cell @@ -67816,7 +67937,7 @@ radial glial cells acting as neural progenitors throughout life. A conventional thymic dendritic cell that is CD8alpha-negative. - 2010-11-23T10:58:53Z + 2010-11-23T10:58:53Z DC.8-.Th CD8alpha-negative thymic conventional dendritic cell @@ -67868,7 +67989,7 @@ radial glial cells acting as neural progenitors throughout life. A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue. - 2010-11-23T01:32:43Z + 2010-11-23T01:32:43Z CD103-positive dendritic cell @@ -67928,7 +68049,7 @@ radial glial cells acting as neural progenitors throughout life. A F4/80-negative dendritic cell located in adipose tissue. - 2010-11-23T01:38:21Z + 2010-11-23T01:38:21Z adipose dendritic cell @@ -67970,7 +68091,7 @@ radial glial cells acting as neural progenitors throughout life. An adipose dendritic cell that is SIRPa-positive. - 2010-11-23T01:40:44Z + 2010-11-23T01:40:44Z DC.SIRPa+.Ad SIRPa-positive adipose dendritic cell @@ -68007,7 +68128,7 @@ radial glial cells acting as neural progenitors throughout life. An adipose dendritic cell that is SIRPa-negative. - 2010-11-23T01:40:46Z + 2010-11-23T01:40:46Z DC.SIRPa-.Ad SIRPa-negative adipose dendritic cell @@ -68044,7 +68165,7 @@ radial glial cells acting as neural progenitors throughout life. A conventional dendritic cell that expresses CD11b (ITGAM). - 2010-11-23T01:50:05Z + 2010-11-23T01:50:05Z CD11b-positive dendritic cell @@ -68116,7 +68237,7 @@ radial glial cells acting as neural progenitors throughout life. A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative. - 2010-11-23T02:00:21Z + 2010-11-23T02:00:21Z DC.11cloSer.SI small intestine serosal dendritic cell @@ -68169,7 +68290,7 @@ radial glial cells acting as neural progenitors throughout life. A myeloid suppressor cell that is Gr1-high and CD11c-negative. - 2010-11-23T02:15:12Z + 2010-11-23T02:15:12Z MDS.Gr1hi Gr1-high myeloid suppressor cell @@ -68222,7 +68343,7 @@ radial glial cells acting as neural progenitors throughout life. A myeloid suppressor cell that is Gr1-low and CD11c-positive. - 2010-11-23T02:19:43Z + 2010-11-23T02:19:43Z MDS.Gr1lo Gr1-low myeloid suppressor cell @@ -68265,7 +68386,7 @@ radial glial cells acting as neural progenitors throughout life. Gr1-high monocyte that lacks MHC-II receptor complex. - 2010-11-23T03:27:12Z + 2010-11-23T03:27:12Z Mo.6C+II- MHC-II-negative classical monocyte @@ -68308,7 +68429,7 @@ radial glial cells acting as neural progenitors throughout life. Gr1-high monocyte that has a MHC-II receptor complex. - 2010-11-23T03:30:21Z + 2010-11-23T03:30:21Z Mo.6c+II MHC-II-positive classical monocyte @@ -68352,7 +68473,7 @@ radial glial cells acting as neural progenitors throughout life. Gr1-low non-classical monocyte that lacks expression of a MHC-II complex. - 2010-11-23T03:38:15Z + 2010-11-23T03:38:15Z Mo.6C-II- MHC-II-negative non-classical monocyte @@ -68395,7 +68516,7 @@ radial glial cells acting as neural progenitors throughout life. Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex. - 2010-11-23T03:47:53Z + 2010-11-23T03:47:53Z Mo.6C-IIint MHC-II-low non-classical monocyte @@ -68438,7 +68559,7 @@ radial glial cells acting as neural progenitors throughout life. Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex. - 2010-11-23T03:47:55Z + 2010-11-23T03:47:55Z Mo.6C-II+ MHC-II-high non-classical monocyte @@ -68501,7 +68622,7 @@ radial glial cells acting as neural progenitors throughout life. A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high. - 2010-11-23T04:00:52Z + 2010-11-23T04:00:52Z lymphoid MHC-II-negative classical monocyte @@ -68563,7 +68684,7 @@ radial glial cells acting as neural progenitors throughout life. A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high. - 2010-11-23T04:09:09Z + 2010-11-23T04:09:09Z lymphoid MHC-II-negative non-classical monocyte @@ -68640,7 +68761,7 @@ radial glial cells acting as neural progenitors throughout life. A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive. - 2010-11-23T04:19:25Z + 2010-11-23T04:19:25Z BTO:0004732 MF.BM bone marrow macrophage @@ -68710,7 +68831,7 @@ radial glial cells acting as neural progenitors throughout life. A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive. - 2010-11-23T04:31:28Z + 2010-11-23T04:31:28Z adipose macrophage @@ -68761,7 +68882,7 @@ radial glial cells acting as neural progenitors throughout life. An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions. - 2010-11-23T04:40:50Z + 2010-11-23T04:40:50Z MF.Autofl.Ad F4/80-negative adipose macrophage @@ -68814,7 +68935,7 @@ radial glial cells acting as neural progenitors throughout life. An adipose macrophage that does not express MHC-II but is F4/80-positive. - 2010-11-23T04:35:53Z + 2010-11-23T04:35:53Z MF.F480+.Ad F4/80-positive adipose macrophage @@ -68849,6 +68970,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -68857,7 +68979,7 @@ radial glial cells acting as neural progenitors throughout life. A goblet cell located in the nasal epithelium. - 2010-12-03T03:03:02Z + 2010-12-03T03:03:02Z MP:0002262 nasal mucosa goblet cell @@ -68890,7 +69012,7 @@ radial glial cells acting as neural progenitors throughout life. The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule. - 2010-12-03T03:11:48Z + 2010-12-03T03:11:48Z peritubular myoid cell @@ -68933,7 +69055,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that produces pigment in the dermis. - 2010-12-03T03:17:05Z + 2010-12-03T03:17:05Z dermal melanocyte @@ -68965,7 +69087,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that produces pigment within the hair follicle. - 2010-12-03T03:17:09Z + 2010-12-03T03:17:09Z hair follicle melanocyte @@ -69001,7 +69123,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that produces pigment in the epithelium. - 2010-12-03T03:17:14Z + 2010-12-03T03:17:14Z The text defintion reference to the MP term appears to reference an epidermal melanocyte term. This term represents any melanocyte in any epithelium. epithelial melanocyte @@ -69045,7 +69167,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. - 2010-12-03T03:25:32Z + 2010-12-03T03:25:32Z retinal melanocyte @@ -69084,7 +69206,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) . - 2010-12-03T03:29:15Z + 2010-12-03T03:29:15Z strial intermediate cell @@ -69103,7 +69225,7 @@ radial glial cells acting as neural progenitors throughout life. A neuronal receptor that respond to mechanical pressure or distortion in the skin. - 2010-12-06T02:53:30Z + 2010-12-06T02:53:30Z cutaneous/subcutaneous mechanoreceptor cell @@ -69149,7 +69271,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta. - 2010-12-06T02:55:24Z + 2010-12-06T02:55:24Z giant trophoblast cell trophoblast giant cell @@ -69204,7 +69326,7 @@ radial glial cells acting as neural progenitors throughout life. A thymocyte that lacks expression of CD4 and CD8. - 2010-12-06T03:03:38Z + 2010-12-06T03:03:38Z CD4-CD8- T cell double negative T cell @@ -69250,7 +69372,7 @@ radial glial cells acting as neural progenitors throughout life. A supporting cell of the organ of Corti. - 2010-12-06T03:09:01Z + 2010-12-06T03:09:01Z organ of Corti supporting cell @@ -69286,7 +69408,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized cell involved in auditory sensory perception. - 2010-12-06T03:18:43Z + 2010-12-06T03:18:43Z auditory epithelial cell @@ -69304,7 +69426,7 @@ radial glial cells acting as neural progenitors throughout life. A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria. - 2010-12-06T03:20:41Z + 2010-12-06T03:20:41Z strial marginal cell @@ -69329,7 +69451,7 @@ radial glial cells acting as neural progenitors throughout life. A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions. - 2010-12-06T03:26:53Z + 2010-12-06T03:26:53Z Basal cells form a multi-layered epithelial barrier that separates the extracellular spaces of the stria vascularis and the spiral ligament[PMID:18353863] strial basal cell @@ -69366,7 +69488,7 @@ radial glial cells acting as neural progenitors throughout life. A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -69390,7 +69512,7 @@ radial glial cells acting as neural progenitors throughout life. A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte. - 2010-12-07T09:50:41Z + 2010-12-07T09:50:41Z embryonic cardiomyocyte neonatal cardiomyocyte @@ -69439,7 +69561,7 @@ radial glial cells acting as neural progenitors throughout life. A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response. - 2010-12-07T09:54:50Z + 2010-12-07T09:54:50Z MESH:D000075942 IEL intraepithelial T cell @@ -69469,7 +69591,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast giant cell derived from the mural trophectoderm. - 2010-12-07T10:07:47Z + 2010-12-07T10:07:47Z EMAPA:16066 primary trophoblast giant cell @@ -69489,7 +69611,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast. - 2010-12-07T10:07:52Z + 2010-12-07T10:07:52Z secondary trophoblast giant cell @@ -69514,7 +69636,7 @@ radial glial cells acting as neural progenitors throughout life. A trophoblast cell that arises in the junctional zone (basal plate) of the placenta. - 2010-12-07T12:56:56Z + 2010-12-07T12:56:56Z spongiotrophoblast spongiotrophoblast cell @@ -69534,7 +69656,7 @@ radial glial cells acting as neural progenitors throughout life. A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide. - 2010-12-07T03:42:06Z + 2010-12-07T03:42:06Z P enteroendocrine cell @@ -69553,7 +69675,7 @@ radial glial cells acting as neural progenitors throughout life. A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide. - 2010-12-07T03:42:09Z + 2010-12-07T03:42:09Z FMA:63207 type D1 enteroendocrine cell @@ -69574,7 +69696,7 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell of the small intestine that secretes motilin. - 2010-12-07T03:55:49Z + 2010-12-07T03:55:49Z Mo enteroendocrine cell FMA:63420 type M enteroendocrine cell @@ -69613,7 +69735,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc - 2010-12-07T04:03:56Z + 2010-12-07T04:03:56Z BTO:0002441 FMA:84639 @@ -69651,7 +69773,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the intestine. - 2011-01-17T03:39:38Z + 2011-01-17T03:39:38Z intestinal smooth muscle cell enteric smooth muscle cell @@ -69734,7 +69856,7 @@ radial glial cells acting as neural progenitors throughout life. A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative. - 2011-01-21T01:27:41Z + 2011-01-21T01:27:41Z DC.103-11b+.Lv liver CD103-negative dendritic cell @@ -69812,7 +69934,7 @@ radial glial cells acting as neural progenitors throughout life. A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver. - 2011-01-21T01:27:45Z + 2011-01-21T01:27:45Z DC.103+11b-.Lv liver CD103-positive dendritic cell @@ -69885,7 +70007,7 @@ radial glial cells acting as neural progenitors throughout life. A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative. - 2011-01-21T01:57:00Z + 2011-01-21T01:57:00Z langerin-positive lymph node dendritic cell @@ -69967,7 +70089,7 @@ radial glial cells acting as neural progenitors throughout life. A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative. - 2011-01-21T02:13:58Z + 2011-01-21T02:13:58Z langerin-negative, CD103-negative lymph node dendritic cell @@ -70015,7 +70137,7 @@ radial glial cells acting as neural progenitors throughout life. A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low. - 2011-01-21T02:07:54Z + 2011-01-21T02:07:54Z CD103-positive, langerin-positive lymph node dendritic cell @@ -70068,7 +70190,7 @@ radial glial cells acting as neural progenitors throughout life. A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high. - 2011-01-21T02:11:14Z + 2011-01-21T02:11:14Z CD103-negative, langerin-positive lymph node dendritic cell @@ -70111,7 +70233,7 @@ radial glial cells acting as neural progenitors throughout life. A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low. - 2011-01-21T02:22:15Z + 2011-01-21T02:22:15Z CD11b-low, CD103-negative, langerin-negative lymph node dendritic cell @@ -70154,7 +70276,7 @@ radial glial cells acting as neural progenitors throughout life. A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high. - 2011-01-21T02:16:21Z + 2011-01-21T02:16:21Z CD11b-high, CD103-negative, langerin-negative lymph node dendritic cell @@ -70179,7 +70301,7 @@ radial glial cells acting as neural progenitors throughout life. A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment. - 2011-01-24T10:22:18Z + 2011-01-24T10:22:18Z tgd.vg5+.IEL Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cell @@ -70199,7 +70321,7 @@ radial glial cells acting as neural progenitors throughout life. A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment. - 2011-01-24T10:25:44Z + 2011-01-24T10:25:44Z tgd.vg5-.IEL Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cell @@ -70220,7 +70342,7 @@ radial glial cells acting as neural progenitors throughout life. An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane. - 2011-02-08T10:11:55Z + 2011-02-08T10:11:55Z interrenal noradrenaline type cell type n interrenal cell interrenal norepinephrine type cell @@ -70242,7 +70364,7 @@ radial glial cells acting as neural progenitors throughout life. A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish. - 2011-02-08T10:21:35Z + 2011-02-08T10:21:35Z interrenal chromaffin cell @@ -70263,7 +70385,7 @@ radial glial cells acting as neural progenitors throughout life. An interrenal chromaffin cell found in teleosts that contain small, homogeneous electron-lucent granules that are separated from the vesicular membrane by a visible halo. - 2011-02-08T10:27:05Z + 2011-02-08T10:27:05Z type a interrenal cell interrenal adrenaline secreting cell interrenal epinephrin secreting cell @@ -70297,7 +70419,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the kidney. - 2011-02-08T10:46:34Z + 2011-02-08T10:46:34Z KUPO:0001019 ZFA:0009374 @@ -70331,7 +70453,7 @@ radial glial cells acting as neural progenitors throughout life. An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type. - 2011-02-08T11:03:32Z + 2011-02-08T11:03:32Z interrenal epithelial cell @@ -70358,7 +70480,7 @@ radial glial cells acting as neural progenitors throughout life. An insect excretory cell that regulates hemolymph composition by filtration and filtrate endocytosis. - 2011-02-08T01:34:56Z + 2011-02-08T01:34:56Z BTO:0004597 nephrocyte @@ -70396,7 +70518,7 @@ radial glial cells acting as neural progenitors throughout life. An adipocyte that is part of subcutaneous adipose tissue. - 2011-02-21T02:51:22Z + 2011-02-21T02:51:22Z subcutaneous fat cell @@ -70429,7 +70551,7 @@ radial glial cells acting as neural progenitors throughout life. A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both. - 2011-02-08T01:37:59Z + 2011-02-08T01:37:59Z renal filtration cell @@ -70464,7 +70586,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros. - 2011-02-08T01:58:30Z + 2011-02-08T01:58:30Z mesonephric glomerular visceral epithelial cell mesonephric podocyte @@ -70490,7 +70612,7 @@ radial glial cells acting as neural progenitors throughout life. A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues. - 2011-02-08T02:07:33Z + 2011-02-08T02:07:33Z disseminated nephrocyte @@ -70526,7 +70648,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the metanephros. - 2011-02-08T02:02:13Z + 2011-02-08T02:02:13Z metanephric glomerular visceral epithelial cell metanephric podocyte @@ -71008,7 +71130,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the cervix. - 2011-02-24T08:20:08Z + 2011-02-24T08:20:08Z cervical canal epithelial cell cervical canal of uterus epithelial cell cervix epithelial cell @@ -71121,7 +71243,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell that is part of the amnion. - 2011-02-28T12:38:01Z + 2011-02-28T12:38:01Z amniotic epithelial cell epithelial cell of amnion @@ -71158,7 +71280,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of the amnion membrane. - 2011-02-28T12:44:24Z + 2011-02-28T12:44:24Z amniotic membrane stem cell amnion mesenchymal stem cell @@ -71196,7 +71318,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. - 2011-02-28T01:20:20Z + 2011-02-28T01:20:20Z ZFA:0009379 small bile duct cholangiocyte @@ -71253,7 +71375,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the aorta. - 2011-02-28T01:42:12Z + 2011-02-28T01:42:12Z BTO:0004577 aortic smooth muscle cell @@ -71285,7 +71407,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell that is part of the bone marrow. - 2011-02-28T01:47:47Z + 2011-02-28T01:47:47Z mesenchymal stem cell of the bone marrow @@ -71320,7 +71442,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of the chorionic membrane. - 2011-02-28T03:04:35Z + 2011-02-28T03:04:35Z chorionic membrane mesenchymal stem cell @@ -71366,7 +71488,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that is part of the vein. - 2011-02-28T03:48:11Z + 2011-02-28T03:48:11Z FMA:62104 KUPO:0001099 endothelial cell of vein @@ -71396,7 +71518,7 @@ radial glial cells acting as neural progenitors throughout life. An arterial endothelial cell that is part of the aorta endothelium. - 2011-02-28T03:54:42Z + 2011-02-28T03:54:42Z BTO:0003245 CALOHA:TS-0047 @@ -71434,7 +71556,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that is part of the thoracic endothelium. - 2011-02-28T03:59:09Z + 2011-02-28T03:59:09Z thoracic aorta endothelial cell @@ -71458,7 +71580,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -71501,7 +71623,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast of the aortic adventitia. - 2011-02-28T04:43:41Z + 2011-02-28T04:43:41Z fibroblast of the aortic adventitia @@ -71543,7 +71665,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast that is part of the heart. - 2011-02-28T04:57:44Z + 2011-02-28T04:57:44Z cardiac fibroblast fibroblast of cardiac tissue @@ -71593,7 +71715,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast that is part of the choroid plexus. - 2011-02-28T05:01:39Z + 2011-02-28T05:01:39Z fibroblast of choroid plexus @@ -71634,7 +71756,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast that is part of the conjuctiva of the eye. - 2011-02-28T05:03:44Z + 2011-02-28T05:03:44Z fibroblast of the conjunctiva @@ -71669,7 +71791,7 @@ radial glial cells acting as neural progenitors throughout life. Any skin fibroblast that is part of some dermis. - 2011-02-28T05:05:33Z + 2011-02-28T05:05:33Z fibroblast of dermis @@ -71710,7 +71832,7 @@ radial glial cells acting as neural progenitors throughout life. Any fibroblast that is part of some gingiva. - 2011-02-28T05:09:12Z + 2011-02-28T05:09:12Z fibroblast of gingiva @@ -71751,7 +71873,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast that is part of lung. - 2011-02-28T05:11:03Z + 2011-02-28T05:11:03Z BTO:0000764 CALOHA:TS-0575 @@ -71795,7 +71917,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast of the lymphatic system. - 2011-02-28T05:16:18Z + 2011-02-28T05:16:18Z fibroblast of lymphatic vessel @@ -71836,7 +71958,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast that is part of the mammary gland. - 2011-02-28T05:18:38Z + 2011-02-28T05:18:38Z fibroblast of mammary gland @@ -71878,7 +72000,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast of the periodontium. - 2011-02-28T05:19:48Z + 2011-02-28T05:19:48Z fibroblast of periodontium @@ -71920,7 +72042,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast of pulmonary artery. - 2011-02-28T05:22:27Z + 2011-02-28T05:22:27Z fibroblast of pulmonary artery @@ -71952,7 +72074,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast that is part of villous mesenchyme. - 2011-02-28T05:24:28Z + 2011-02-28T05:24:28Z fibroblast of villous mesenchyme @@ -71988,7 +72110,7 @@ radial glial cells acting as neural progenitors throughout life. An animal cell that is part of a hair follicle. - 2011-03-01T04:11:01Z + 2011-03-01T04:11:01Z hair follicle cell @@ -72024,7 +72146,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell that resides in the inner root sheath of the hair follicle. - 2011-03-01T04:27:51Z + 2011-03-01T04:27:51Z inner root sheath cell @@ -72066,7 +72188,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell that is part of the outer root sheath. - 2011-03-01T04:29:47Z + 2011-03-01T04:29:47Z outer root sheath cell @@ -72108,7 +72230,7 @@ radial glial cells acting as neural progenitors throughout life. An epidermal cell that is part of the germinal matrix. - 2011-03-01T04:31:06Z + 2011-03-01T04:31:06Z trichocyte hair germinal matrix cell @@ -72150,7 +72272,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the intestine. - 2011-03-01T05:18:31Z + 2011-03-01T05:18:31Z ZFA:0009399 intestinal epithelial cell @@ -72193,7 +72315,7 @@ radial glial cells acting as neural progenitors throughout life. A connective tissue cell of the nucleus pulposus cell of intervertebral disc. - 2011-03-02T02:12:23Z + 2011-03-02T02:12:23Z nucleus pulposus cell of intervertebral disc @@ -72230,7 +72352,7 @@ radial glial cells acting as neural progenitors throughout life. A pigment cell located in the epithelium of the iris. - 2011-03-01T05:28:52Z + 2011-03-01T05:28:52Z iris pigment epithelial cell @@ -72256,7 +72378,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that appears darker due to content or amount of melanin granules. - 2011-03-01T05:57:11Z + 2011-03-01T05:57:11Z melanotic melanocyte melanotic melanophore dark melanocyte @@ -72288,7 +72410,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte that appears lighter in color. - 2011-03-01T05:58:23Z + 2011-03-01T05:58:23Z amelanotic melanocyte amelanotic melanophore light melanocyte @@ -72321,7 +72443,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell that is part of Wharton's jelly. - 2011-03-01T09:51:18Z + 2011-03-01T09:51:18Z mesenchymal stem cell of Wharton's jelly @@ -72358,7 +72480,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of the umbilical cord. - 2011-03-01T09:55:12Z + 2011-03-01T09:55:12Z mesenchymal stem cell of umbilical cord @@ -72393,7 +72515,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of adipose tissue. - 2011-03-01T09:57:17Z + 2011-03-01T09:57:17Z mesenchymal stem cell of adipose mesenchymal stem cell of adipose tissue @@ -72425,7 +72547,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of liver. - 2011-03-01T09:58:51Z + 2011-03-01T09:58:51Z hepatic mesenchymal stem cell @@ -72467,7 +72589,7 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of the vertebrae. - 2011-03-01T10:40:27Z + 2011-03-01T10:40:27Z vertebral mesenchymal stem cell @@ -72498,7 +72620,7 @@ radial glial cells acting as neural progenitors throughout life. A glial cell that myelinates or ensheathes axons in the peripheral nervous system. - 2011-03-02T01:19:27Z + 2011-03-02T01:19:27Z BTO:0001220 CALOHA:TS-0898 MESH:D012583 @@ -72547,7 +72669,7 @@ radial glial cells acting as neural progenitors throughout life. A stromal cell of the pancreas. - 2011-03-02T02:40:41Z + 2011-03-02T02:40:41Z stromal cell of pancreas @@ -72590,7 +72712,7 @@ radial glial cells acting as neural progenitors throughout life. A pericyte of the central nervous system. - 2011-03-02T02:54:18Z + 2011-03-02T02:54:18Z central nervous system pericyte @@ -72622,7 +72744,7 @@ radial glial cells acting as neural progenitors throughout life. A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot. - 2011-03-02T03:03:58Z + 2011-03-02T03:03:58Z perineurial glial cell There are studies that largely accept the idea that the perineurial cell is a modified fibroblast with myofibroblastic features. @@ -72677,7 +72799,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the placenta. - 2011-03-02T03:21:30Z + 2011-03-02T03:21:30Z placental epithelial cell @@ -72718,7 +72840,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte found in mesenteric tissue. - 2011-03-03T04:19:40Z + 2011-03-03T04:19:40Z mesenteric preadipocyte @@ -72759,7 +72881,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte that is part of an omentum. - 2011-03-03T04:19:42Z + 2011-03-03T04:19:42Z omentum preadipocyte @@ -72795,7 +72917,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte that is part of the breast. - 2011-03-03T04:19:46Z + 2011-03-03T04:19:46Z preadipocyte of the breast @@ -72836,7 +72958,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte that is part of a perirenal fat tissue. - 2011-03-03T04:20:04Z + 2011-03-03T04:20:04Z perirenal preadipocyte @@ -72861,7 +72983,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte that is part of visceral tissue. - 2011-03-03T04:32:56Z + 2011-03-03T04:32:56Z visceral preadipocyte @@ -72896,7 +73018,7 @@ radial glial cells acting as neural progenitors throughout life. A preadipocyte that is part of subcutaneous tissue. - 2011-03-03T04:33:01Z + 2011-03-03T04:33:01Z subcutaneous preadipocyte @@ -72980,7 +73102,7 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. - 2011-03-06T03:28:27Z + 2011-03-06T03:28:27Z @@ -73033,7 +73155,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. - 2011-03-06T03:37:09Z + 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 @@ -73083,7 +73205,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the umbilical vein. - 2011-03-06T05:00:51Z + 2011-03-06T05:00:51Z smooth muscle cell of the umbilical vein @@ -73118,7 +73240,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the bachiocephalic vasculature. - 2011-03-06T05:00:58Z + 2011-03-06T05:00:58Z smooth muscle cell of the brachiocephalic vasculature @@ -73154,7 +73276,7 @@ radial glial cells acting as neural progenitors throughout life. A vascular associated smooth muscle cell of the brain vasculature. - 2011-03-06T05:01:20Z + 2011-03-06T05:01:20Z smooth muscle cell of the brain vasculature @@ -73196,7 +73318,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle of the pulmonary artery. - 2011-03-06T05:01:28Z + 2011-03-06T05:01:28Z BTO:0003336 @@ -73236,7 +73358,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the coronary artery. - 2011-03-06T05:01:34Z + 2011-03-06T05:01:34Z smooth muscle cell of the coronary artery @@ -73272,7 +73394,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle of the internal thoracic artery. - 2011-03-06T05:01:41Z + 2011-03-06T05:01:41Z smooth muscle cell of the internal thoracic artery @@ -73307,7 +73429,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the umbilical artery. - 2011-03-06T05:01:48Z + 2011-03-06T05:01:48Z smooth muscle cell of the umbilical artery @@ -73342,7 +73464,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the subclavian artery. - 2011-03-06T05:01:52Z + 2011-03-06T05:01:52Z smooth muscle cell of the subclavian artery @@ -73377,7 +73499,7 @@ radial glial cells acting as neural progenitors throughout life. Smooth muscle cell of the carotid artery. - 2011-03-06T05:01:56Z + 2011-03-06T05:01:56Z smooth muscle cell of the carotid artery @@ -73408,7 +73530,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the bladder. - 2011-03-06T05:43:24Z + 2011-03-06T05:43:24Z KUPO:0001122 smooth muscle cell of bladder @@ -73452,7 +73574,7 @@ radial glial cells acting as neural progenitors throughout life. Any smooth muscle cell that is part of some bronchus. - 2011-03-06T05:46:39Z + 2011-03-06T05:46:39Z BTO:0004402 @@ -73490,7 +73612,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the esophagus. - 2011-03-06T05:48:17Z + 2011-03-06T05:48:17Z smooth muscle cell of the esophagus @@ -73531,7 +73653,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the trachea. - 2011-03-06T05:50:28Z + 2011-03-06T05:50:28Z smooth muscle cell of trachea @@ -73567,7 +73689,7 @@ radial glial cells acting as neural progenitors throughout life. A smooth muscle cell of the uterus. - 2011-03-06T05:53:28Z + 2011-03-06T05:53:28Z uterine smooth muscle cell @@ -73609,7 +73731,7 @@ radial glial cells acting as neural progenitors throughout life. Any connective tissue cell that is part of some annulus fibrosus disci intervertebralis. - 2011-03-06T06:50:53Z + 2011-03-06T06:50:53Z anulus pulposus cell annulus pulposus cell @@ -73652,7 +73774,7 @@ radial glial cells acting as neural progenitors throughout life. An astrocyte of the cerebellum. - 2011-03-06T06:57:27Z + 2011-03-06T06:57:27Z astrocyte of the cerebellum @@ -73690,7 +73812,7 @@ radial glial cells acting as neural progenitors throughout life. An astrocyte that is part of the hippocampus. - 2011-03-06T06:57:33Z + 2011-03-06T06:57:33Z astrocyte of the hippocampal formation astrocyte of the hippocampus @@ -73724,7 +73846,7 @@ radial glial cells acting as neural progenitors throughout life. An astrocyte of the cerebral cortex. - 2011-03-06T06:57:36Z + 2011-03-06T06:57:36Z astrocyte of the cerebral cortex @@ -73761,7 +73883,7 @@ radial glial cells acting as neural progenitors throughout life. An astrocyte of the spinal cord. - 2011-03-06T07:11:26Z + 2011-03-06T07:11:26Z astrocyte of the spinal cord @@ -73785,7 +73907,7 @@ radial glial cells acting as neural progenitors throughout life. A neural crest cell that gives rise to cells of the enteric nervous system. - 2011-03-06T07:24:35Z + 2011-03-06T07:24:35Z migratory enteric neural crest cell @@ -73821,7 +73943,7 @@ radial glial cells acting as neural progenitors throughout life. A neuron with a soma found in the hippocampus. - 2011-03-06T07:31:49Z + 2011-03-06T07:31:49Z hippocampal neuron @@ -73841,7 +73963,7 @@ radial glial cells acting as neural progenitors throughout life. - 2011-03-06T07:37:08Z + 2011-03-06T07:37:08Z BTO:0004102 FMA:84104 cortical neuron @@ -73881,7 +74003,7 @@ radial glial cells acting as neural progenitors throughout life. A neuron of the raphe nuclei. - 2011-03-06T07:42:06Z + 2011-03-06T07:42:06Z raphe nuclei neuron @@ -73923,7 +74045,7 @@ radial glial cells acting as neural progenitors throughout life. A CNS neuron of the dorsal spinal cord. - 2011-03-06T07:43:34Z + 2011-03-06T07:43:34Z neuron of the dorsal spinal cord @@ -73965,7 +74087,7 @@ radial glial cells acting as neural progenitors throughout life. A neuron of the ventral spinal cord. - 2011-03-06T07:46:03Z + 2011-03-06T07:46:03Z neuron of the ventral spinal cord @@ -74006,7 +74128,7 @@ radial glial cells acting as neural progenitors throughout life. A neuron of the striatum. - 2011-03-06T07:47:12Z + 2011-03-06T07:47:12Z striatum neuron @@ -74042,7 +74164,7 @@ radial glial cells acting as neural progenitors throughout life. A neuron of the substantia nigra. - 2011-03-06T07:48:42Z + 2011-03-06T07:48:42Z neuron of the substantia nigra @@ -74083,7 +74205,7 @@ radial glial cells acting as neural progenitors throughout life. An adipocyte that is part of omentum tissue. - 2011-03-14T10:17:00Z + 2011-03-14T10:17:00Z omental adipocyte omental fat cell adipocyte of omentum tissue @@ -74126,7 +74248,7 @@ radial glial cells acting as neural progenitors throughout life. An adipocyte of perirenal fat tissue. - 2011-03-14T10:17:05Z + 2011-03-14T10:17:05Z perirenal adipocyte cell perirenal fat cell perirenal adipocyte @@ -74169,7 +74291,7 @@ radial glial cells acting as neural progenitors throughout life. An adipocyte that is part of the breast. - 2011-03-14T10:17:07Z + 2011-03-14T10:17:07Z CALOHA:TS-2377 breast adipocyte fat cell of breast @@ -74215,7 +74337,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the umbilical vein. - 2011-03-14T11:36:51Z + 2011-03-14T11:36:51Z BTO:0004296 endothelial cell of umbilical vein @@ -74235,7 +74357,7 @@ radial glial cells acting as neural progenitors throughout life. An adult angioblastic cell released from the bone marrow, or from the kidney in some teleost species, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. - 2011-03-14T12:11:18Z + 2011-03-14T12:11:18Z EPC The existence of adult endothelial progenitor cells has been controversial in the past. @@ -74279,7 +74401,7 @@ radial glial cells acting as neural progenitors throughout life. A fibroblast of skin. - 2011-03-14T12:31:49Z + 2011-03-14T12:31:49Z BTO:0001255 CALOHA:TS-0935 @@ -74324,7 +74446,7 @@ radial glial cells acting as neural progenitors throughout life. Any epithelial cell that is part of some gingival epithelium. - 2011-03-14T12:46:28Z + 2011-03-14T12:46:28Z gingival epithelial cell @@ -74359,7 +74481,7 @@ radial glial cells acting as neural progenitors throughout life. A stromal cell of the prostate. - 2011-03-14T02:11:10Z + 2011-03-14T02:11:10Z BTO:0003972 prostate stromal cell @@ -74397,7 +74519,7 @@ radial glial cells acting as neural progenitors throughout life. An acinar cell of salivary gland. - 2011-03-14T02:22:22Z + 2011-03-14T02:22:22Z acinar cell of salivary gland @@ -74434,7 +74556,7 @@ radial glial cells acting as neural progenitors throughout life. A paneth cell of the appendix. - 2011-03-15T09:38:18Z + 2011-03-15T09:38:18Z paneth cell of the appendix @@ -74476,7 +74598,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the seminiferous tubule epithelium. - 2011-03-15T11:59:23Z + 2011-03-15T11:59:23Z seminiferous tubule epithelial cell @@ -74663,7 +74785,7 @@ radial glial cells acting as neural progenitors throughout life. A spore formed from bacteria in the order Actinomycetales. - 2011-06-16T01:01:41Z + 2011-06-16T01:01:41Z actinomycete-type spore @@ -74682,10 +74804,10 @@ radial glial cells acting as neural progenitors throughout life. - + - + @@ -74694,24 +74816,18 @@ radial glial cells acting as neural progenitors throughout life. - + - Any respiratory epithelial cell that is part of some upper respiratory tract. + Any epithelial cell that is part of some upper respiratory tract epithelium. - 2011-06-21T12:28:55Z + 2011-06-21T12:28:55Z epithelial cell of upper respiratory tract - - - - - true - - Any respiratory epithelial cell that is part of some upper respiratory tract. + Any epithelial cell that is part of some upper respiratory tract epithelium. FBC:Autogenerated @@ -74723,10 +74839,10 @@ radial glial cells acting as neural progenitors throughout life. - + - + @@ -74735,25 +74851,19 @@ radial glial cells acting as neural progenitors throughout life. - + - Any respiratory epithelial cell that is part of some lower respiratory tract. + Any epithelial cell that is part of some lower respiratory tract epithelium. - 2011-06-21T12:29:31Z + 2011-06-21T12:29:31Z epithelial cell of lower respiratory tract - - - - - true - - Any respiratory epithelial cell that is part of some lower respiratory tract. + Any epithelial cell that is part of some lower respiratory tract epithelium. FBC:Autogenerated @@ -74762,11 +74872,27 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + - + + + + + + A basal cell in the respiratory tract. - 2011-06-21T03:11:10Z + 2011-06-21T03:11:10Z airway basal cell airway basal stem cell @@ -74805,7 +74931,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the anal column. - 2011-07-08T12:11:38Z + 2011-07-08T12:11:38Z epithelial cell of anal column @@ -74823,7 +74949,7 @@ radial glial cells acting as neural progenitors throughout life. A nonkeratinized epithelial cell of the anal canal. - 2011-07-08T02:05:33Z + 2011-07-08T02:05:33Z FMA:263146 nonkeratinized epithelial cell of anal column @@ -74843,7 +74969,7 @@ radial glial cells acting as neural progenitors throughout life. A nonkeratinized cell epithleial cell of the inferior part of the anal canal. - 2011-07-08T02:06:53Z + 2011-07-08T02:06:53Z FMA:263144 nonkeratinized epithelial cell of inferior part of anal canal @@ -74875,7 +75001,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal. - 2011-07-08T02:08:40Z + 2011-07-08T02:08:40Z keratinized epithelial cell of the anal canal @@ -74890,31 +75016,33 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc. - 2011-06-21T03:26:08Z + 2011-06-21T03:26:08Z BASC basal epithelial cell of bronchioalveolar duct junction bronchioalveolar stem cell + + + + + true + @@ -74933,7 +75061,7 @@ radial glial cells acting as neural progenitors throughout life. An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone - 2011-06-21T03:55:39Z + 2011-06-21T03:55:39Z Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. amniotic stem cell @@ -74953,7 +75081,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial fate stem cell derived form the amnion membrane. - 2011-06-21T04:06:17Z + 2011-06-21T04:06:17Z amniotic epithelial stem cell @@ -74972,7 +75100,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the esophageal gland proper. - 2011-07-08T02:16:51Z + 2011-07-08T02:16:51Z FMA:256141 epithelial cell of esophageal gland proper @@ -74991,7 +75119,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia. - 2011-07-08T02:16:54Z + 2011-07-08T02:16:54Z FMA:256143 epithelial cell of esophageal cardiac gland @@ -75011,7 +75139,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin. - 2011-07-08T02:22:09Z + 2011-07-08T02:22:09Z FMA:263148 nonkeratinized cell of stratum corneum of esophageal epithelium @@ -75030,7 +75158,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa. - 2011-07-08T02:25:44Z + 2011-07-08T02:25:44Z FMA:70628 endo-epithelial cell of tympanic part of viscerocranial mucosa @@ -75049,7 +75177,7 @@ radial glial cells acting as neural progenitors throughout life. An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa. - 2011-07-08T02:25:46Z + 2011-07-08T02:25:46Z FMA:70629 endo-epithelial cell of pharyngotympanic part of viscerocranial mucosa @@ -75067,7 +75195,7 @@ radial glial cells acting as neural progenitors throughout life. An ecto-epithelial cell of the buccal region of the viscerocranial mucosa. - 2011-07-08T02:34:12Z + 2011-07-08T02:34:12Z FMA:70577 obsolete epithelial cell of buccal part of viscerocranial mucosa true @@ -75086,7 +75214,7 @@ radial glial cells acting as neural progenitors throughout life. An ecto-epithelial cell of the palatal region of the viscerocranial mucosa. - 2011-07-08T02:34:14Z + 2011-07-08T02:34:14Z FMA:70580 obsolete epithelial cell of anterior palatal part of viscerocranial mucosa true @@ -75105,7 +75233,7 @@ radial glial cells acting as neural progenitors throughout life. An ecto-epithelial cell of the nasal region of the viscerocranial mucosa. - 2011-07-08T02:36:06Z + 2011-07-08T02:36:06Z FMA:70554 obsolete epithelial cell of nasal part of viscerocranial mucosa true @@ -75124,7 +75252,7 @@ radial glial cells acting as neural progenitors throughout life. An ecto-epithelial cell of the gingival region of the viscerocranial mucosa. - 2011-07-08T02:36:11Z + 2011-07-08T02:36:11Z FMA:70579 obsolete epithelial cell of gingival part of viscerocranial mucosa true @@ -75143,7 +75271,7 @@ radial glial cells acting as neural progenitors throughout life. An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa. - 2011-07-08T02:38:18Z + 2011-07-08T02:38:18Z FMA:70578 obsolete epithelial cell of paranasal sinus part of viscerocranial mucosa true @@ -75163,7 +75291,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits. - 2011-07-08T03:06:49Z + 2011-07-08T03:06:49Z FMA:72140 stave cell endothelial cell of venous sinus of spleen @@ -75189,7 +75317,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -75197,7 +75325,6 @@ radial glial cells acting as neural progenitors throughout life. - @@ -75208,7 +75335,7 @@ radial glial cells acting as neural progenitors throughout life. A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream. - 2011-07-08T03:14:10Z + 2011-07-08T03:14:10Z endothelial cell of postcapillary venule of lymph node FMA:67759 HEV cell @@ -75229,18 +75356,17 @@ radial glial cells acting as neural progenitors throughout life. - - - A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. + + A squamous shaped endothelial cell. - 2011-07-08T03:31:25Z + 2011-07-08T03:31:25Z squamous endothelial cell - A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. - GOC:tfm + A squamous shaped endothelial cell. + GOC:dos @@ -75251,7 +75377,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of stratum corneum of esophageal epithelium. - 2011-07-08T03:46:35Z + 2011-07-08T03:46:35Z FMA:70733 epithelial cell of stratum corneum of esophageal epithelium @@ -75270,7 +75396,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of stratum spinosum of esophageal epithelium. - 2011-07-08T03:48:26Z + 2011-07-08T03:48:26Z FMA:70732 epithelial cell of stratum spinosum of esophageal epithelium @@ -75306,7 +75432,7 @@ radial glial cells acting as neural progenitors throughout life. A glandular epithelial cell of the endometrium. - 2011-07-08T03:54:08Z + 2011-07-08T03:54:08Z FMA:86489 glandular cell of endometrium @@ -75337,7 +75463,7 @@ radial glial cells acting as neural progenitors throughout life. A glandular epithelial cell of the esophagus. - 2011-07-08T03:55:57Z + 2011-07-08T03:55:57Z FMA:86548 glandular cell of esophagus @@ -75381,7 +75507,7 @@ radial glial cells acting as neural progenitors throughout life. A glandular epithelial cell of the large intestine. - 2011-07-08T04:03:01Z + 2011-07-08T04:03:01Z FMA:87194 glandular cell of the large intestine @@ -75418,7 +75544,7 @@ radial glial cells acting as neural progenitors throughout life. A glandular epithelial cell that is part of the stomach. - 2011-07-11T01:20:35Z + 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 glandular cell of stomach @@ -75444,7 +75570,7 @@ radial glial cells acting as neural progenitors throughout life. A luminal epithelial cell of mammary gland located in acinus of structure. - 2011-07-11T01:44:31Z + 2011-07-11T01:44:31Z FMA:74505 Consider if synonymous with mammary alveolar cell CL:0002325. Some use this term to refer to the non-lactating cell type that gives rise to the lactating cell type. luminal cell of acinus of lactiferous gland @@ -75464,7 +75590,7 @@ radial glial cells acting as neural progenitors throughout life. A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into. - 2011-07-11T01:44:33Z + 2011-07-11T01:44:33Z FMA:87168 luminal cell of lactiferous terminal ductal lobular unit @@ -75483,7 +75609,7 @@ radial glial cells acting as neural progenitors throughout life. A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive. - 2011-07-11T01:44:48Z + 2011-07-11T01:44:48Z FMA:74504 luminal cell of lactiferous duct @@ -75520,7 +75646,7 @@ radial glial cells acting as neural progenitors throughout life. A myocardial endocrine cell that is part of the atrium. - 2011-07-11T02:45:39Z + 2011-07-11T02:45:39Z FMA:83389 myocardial endocrine cell of atrium @@ -75545,7 +75671,7 @@ radial glial cells acting as neural progenitors throughout life. A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart. - 2011-07-11T03:15:38Z + 2011-07-11T03:15:38Z cardiovascular progenitor cell CPC Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell. @@ -75587,7 +75713,7 @@ radial glial cells acting as neural progenitors throughout life. A fibrocyte of the cochlea that has specialized structural and molecular adaptions. - 2011-07-11T03:35:01Z + 2011-07-11T03:35:01Z otic fibrocyte @@ -75606,7 +75732,7 @@ radial glial cells acting as neural progenitors throughout life. An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. - 2011-07-11T03:40:40Z + 2011-07-11T03:40:40Z type II otic fibrocyte type II spiral ligament fibrocyte type 2 otic fibrocyte @@ -75633,7 +75759,7 @@ radial glial cells acting as neural progenitors throughout life. An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. - 2011-07-11T03:40:42Z + 2011-07-11T03:40:42Z type V otic fibrocyte type V spiral ligament fibrocyte type 5 otic fibrocyte @@ -75654,7 +75780,7 @@ radial glial cells acting as neural progenitors throughout life. An otic fibrocyte that is lateral to the basilar membrane and anchoris it to the lateral wall. - 2011-07-11T03:40:46Z + 2011-07-11T03:40:46Z type IV otic fibrocyte type IV spiral ligament fibrocyte type 4 otic fibrocyte @@ -75681,17 +75807,11 @@ radial glial cells acting as neural progenitors throughout life. An otic fibrocyte that lines the otic capsule. - 2011-07-11T03:40:50Z + 2011-07-11T03:40:50Z type III otic fibrocyte type III spiral ligament fibrocyte type 3 otic fibrocyte - - - - type III spiral ligament fibrocyte - MP:0004489 - @@ -75699,6 +75819,12 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:18353863 + + + + type III spiral ligament fibrocyte + MP:0004489 + @@ -75708,7 +75834,7 @@ radial glial cells acting as neural progenitors throughout life. An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph. - 2011-07-11T03:39:27Z + 2011-07-11T03:39:27Z type I otic fibrocyte type I spiral ligament fibrocyte type 1 otic fibrocyte @@ -75735,7 +75861,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout. - 2011-08-16T01:49:32Z + 2011-08-16T01:49:32Z endothelial stalk cell @@ -75762,7 +75888,7 @@ radial glial cells acting as neural progenitors throughout life. A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. - 2011-08-16T02:38:01Z + 2011-08-16T02:38:01Z retinal progenitor cell @@ -75799,7 +75925,7 @@ radial glial cells acting as neural progenitors throughout life. A skeletal muscle cell that is part of the tongue. - 2011-08-16T03:10:02Z + 2011-08-16T03:10:02Z tongue muscle cell @@ -75825,7 +75951,7 @@ radial glial cells acting as neural progenitors throughout life. A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. - 2011-08-16T03:20:53Z + 2011-08-16T03:20:53Z H- cell H minus @@ -75850,7 +75976,7 @@ radial glial cells acting as neural progenitors throughout life. A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus. - 2011-08-16T03:20:58Z + 2011-08-16T03:20:58Z H plus @@ -75875,7 +76001,7 @@ radial glial cells acting as neural progenitors throughout life. A neuroblast derived from a neural crest cell. - 2011-08-22T09:24:15Z + 2011-08-22T09:24:15Z neural crest derived neuroblast @@ -75896,7 +76022,7 @@ radial glial cells acting as neural progenitors throughout life. A regulatory T cell that has not encountered antigen. - 2011-08-25T03:17:21Z + 2011-08-25T03:17:21Z naive regulatory T lymphocyte naive regulatory T-cell naive regulatory T-lymphocyte @@ -75932,7 +76058,7 @@ radial glial cells acting as neural progenitors throughout life. A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen. - 2011-08-25T03:17:34Z + 2011-08-25T03:17:34Z Cell has been described as being CD45RA-positive in human, but this doesn't fit with our current definition memory T cell. memory regulatory T cell @@ -76060,7 +76186,7 @@ radial glial cells acting as neural progenitors throughout life. A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13 - 2011-08-29T10:08:02Z + 2011-08-29T10:08:02Z natural helper lymphocyte @@ -76098,7 +76224,7 @@ radial glial cells acting as neural progenitors throughout life. A PP cell found in intestine. - 2011-09-27T11:59:01Z + 2011-09-27T11:59:01Z PP cell of intestine @@ -76141,7 +76267,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of a cortex of kidney. - 2011-10-25T03:49:41Z + 2011-10-25T03:49:41Z kidney cortical cell @@ -80010,7 +80136,7 @@ radial glial cells acting as neural progenitors throughout life. Lymphatic progenitor cells. - 2012-01-12T04:44:34Z + 2012-01-12T04:44:34Z ZFA:0009393 Usually express Prox1, or prox1b. lymphangioblast @@ -80043,7 +80169,7 @@ radial glial cells acting as neural progenitors throughout life. Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics. - 2012-01-12T05:01:22Z + 2012-01-12T05:01:22Z ZFA:0009394 mesenchymal lymphangioblast @@ -80087,7 +80213,7 @@ radial glial cells acting as neural progenitors throughout life. Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. - 2012-01-12T05:21:09Z + 2012-01-12T05:21:09Z ZFA:0009395 parachordal lymphangioblast @@ -80278,7 +80404,7 @@ radial glial cells acting as neural progenitors throughout life. Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins. - 2012-06-15T01:27:01Z + 2012-06-15T01:27:01Z unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 preameloblast @@ -80298,7 +80424,7 @@ radial glial cells acting as neural progenitors throughout life. Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). - 2012-06-15T02:51:27Z + 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -80330,7 +80456,7 @@ radial glial cells acting as neural progenitors throughout life. Skeletogenic cell that has the potential to develop into a cementoblast. - 2012-06-15T04:37:13Z + 2012-06-15T04:37:13Z precementoblast @@ -80361,7 +80487,7 @@ radial glial cells acting as neural progenitors throughout life. Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell. - 2012-06-15T05:15:11Z + 2012-06-15T05:15:11Z preodontoblast @@ -80392,7 +80518,7 @@ radial glial cells acting as neural progenitors throughout life. Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -80430,7 +80556,7 @@ radial glial cells acting as neural progenitors throughout life. Cell that is part of the notochord. - 2012-06-27T08:47:31Z + 2012-06-27T08:47:31Z NOTE: TO DO, notochord development still needs work. notochordal cell @@ -80455,7 +80581,7 @@ radial glial cells acting as neural progenitors throughout life. Mesodermal cell that is axially located and gives rise to the cells of the notochord. - 2012-06-27T08:52:41Z + 2012-06-27T08:52:41Z axial mesodermal cell chordamesodermal cell @@ -80474,7 +80600,7 @@ radial glial cells acting as neural progenitors throughout life. Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells. - 2012-06-27T09:26:37Z + 2012-06-27T09:26:37Z ZFA:0005744 notochordal sheath cell @@ -80499,7 +80625,7 @@ radial glial cells acting as neural progenitors throughout life. Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds. - 2012-06-27T09:29:30Z + 2012-06-27T09:29:30Z chordablast chordoblast notochordal vacuole cell @@ -80531,7 +80657,7 @@ radial glial cells acting as neural progenitors throughout life. Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. - 2012-06-27T10:44:01Z + 2012-06-27T10:44:01Z prechondroblast @@ -80570,7 +80696,7 @@ radial glial cells acting as neural progenitors throughout life. Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells. - 2012-06-27T10:57:21Z + 2012-06-27T10:57:21Z osteoprogenitor cell preosteoblast @@ -80620,7 +80746,7 @@ radial glial cells acting as neural progenitors throughout life. Neuron that is part of the enteric nervous system. - 2012-06-28T08:20:31Z + 2012-06-28T08:20:31Z ZFA:0005775 enteric neuron @@ -80679,7 +80805,7 @@ radial glial cells acting as neural progenitors throughout life. OBSOLETE: A cultured cell that has been passaged at least one time in culture. - 2012-11-28T11:54:59Z + 2012-11-28T11:54:59Z passaged cultured cell Obsoleted in July 2013 and replaced by the CLO 'cell line cell' class, as a result of CLO-OBI-CL alignment efforts. @@ -80702,7 +80828,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u OBSOLETE: A cell line cell that is expected to be capable of replicating a limited number of times in culture before undergoing senescence. Mortal cell line cells cannot be propagated indefinitely (as immortal cell line cells can). - 2012-11-28T11:56:20Z + 2012-11-28T11:56:20Z finite cell line cell primary cell line cell Obsoleted in July 2013 and replaced by the CLO 'mortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts. @@ -80732,7 +80858,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm. - 2012-12-30T12:43:15Z + 2012-12-30T12:43:15Z ZFA:0000003 In teleosts, adaxial cells give rise to slow muscle myoblasts. adaxial cell @@ -81384,18 +81510,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage. activated skeletal muscle satellite cell - + - + More accurately - transformation_of ? @@ -82086,6 +82212,25 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. + 2024-07-03T19:52:47Z + + squamous endothelial cell of venule + + + + + An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. + GOC:tfm + + + + @@ -85110,6 +85255,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u 2021-11-25T09:30:45Z + There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. committed double negative thymocyte (Homo sapiens) @@ -85217,7 +85363,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -85394,7 +85540,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + + + + + An endothelial cell that is part of a placenta. 2021-12-13T13:53:01Z @@ -85467,7 +85618,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -85942,7 +86093,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -85972,7 +86122,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -86002,7 +86151,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -86033,7 +86181,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -86196,19 +86343,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + - - - - - - An endothelial cell located in a lymph node lymphatic vessel. @@ -86343,7 +86484,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -86534,19 +86675,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -87493,15 +87634,15 @@ Covers cells actively being cultured or stored in a quiescent state for future u + An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential. - An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential. Tex cell exhausted T cell - + An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential. PMID:26544946 @@ -87581,15 +87722,15 @@ Covers cells actively being cultured or stored in a quiescent state for future u + A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons. BTO:0002771 - A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons. OEC olfactory ensheathing cell - + A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons. PMID:22456085 @@ -88337,6 +88478,17 @@ plexiform layer using GABA. + + + + + + + + + + + An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice. @@ -88684,7 +88836,7 @@ plexiform layer using GABA. Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. - 2010-05-25T01:36:34Z + 2010-05-25T01:36:34Z neutrophillic cytoplasm @@ -88703,7 +88855,7 @@ plexiform layer using GABA. - 2009-12-22T03:54:43Z + 2009-12-22T03:54:43Z Obsoleted because duplicate with GO term. obsolete lobed nucleus true @@ -88740,7 +88892,7 @@ plexiform layer using GABA. Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -88776,7 +88928,7 @@ plexiform layer using GABA. Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -88811,7 +88963,7 @@ plexiform layer using GABA. Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -88830,7 +88982,7 @@ plexiform layer using GABA. - 2009-12-23T10:53:24Z + 2009-12-23T10:53:24Z This class was a phenotype, not a cell type. obsolete increased nucleus size true @@ -88850,7 +89002,7 @@ plexiform layer using GABA. A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament. - 2009-12-23T02:18:43Z + 2009-12-23T02:18:43Z banded nucleus @@ -88885,7 +89037,7 @@ plexiform layer using GABA. A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin. - 2009-12-23T02:31:25Z + 2009-12-23T02:31:25Z reniform nucleus @@ -88903,7 +89055,7 @@ plexiform layer using GABA. Heterochromatin that is arranged in a carthwheel pattern. - 2009-12-28T04:28:35Z + 2009-12-28T04:28:35Z cartwheel heterochromatin @@ -89022,7 +89174,7 @@ plexiform layer using GABA. - + @@ -89896,7 +90048,7 @@ plexiform layer using GABA. - + @@ -89904,14 +90056,14 @@ plexiform layer using GABA. - Any goblet cell that is part of some lung. + Any goblet cell that is part of some lung epithelium. lung goblet cell - Any goblet cell that is part of some lung. + Any goblet cell that is part of some lung epithelium. FBC:Autogenerated @@ -90133,7 +90285,6 @@ plexiform layer using GABA. - @@ -92711,6 +92862,7 @@ plexiform layer using GABA. A columnar cell of the colon that is part of the colonic epithelium. FMA:263114 + colonocyte vacuolar absorptive cell of epithelium of colon enterocyte of colon @@ -92727,6 +92879,12 @@ plexiform layer using GABA. A columnar cell of the colon that is part of the colonic epithelium. GOC:tfm + + + + colonocyte + PMID:34497389 + @@ -92744,7 +92902,6 @@ plexiform layer using GABA. - @@ -92821,8 +92978,6 @@ plexiform layer using GABA. - - @@ -92865,8 +93020,6 @@ plexiform layer using GABA. - - @@ -92909,8 +93062,6 @@ plexiform layer using GABA. - - @@ -94117,6 +94268,7 @@ plexiform layer using GABA. + @@ -94453,7 +94605,6 @@ plexiform layer using GABA. - @@ -94576,7 +94727,7 @@ plexiform layer using GABA. - + @@ -94590,12 +94741,6 @@ plexiform layer using GABA. endothelial cell of venule - - - - - true - @@ -96904,7 +97049,6 @@ plexiform layer using GABA. - @@ -97563,12 +97707,6 @@ plexiform layer using GABA. kidney corpuscule cell - - - - - true - @@ -98511,12 +98649,6 @@ plexiform layer using GABA. KUPO:0001036 glomerular cell - - - - - true - @@ -98676,31 +98808,29 @@ plexiform layer using GABA. + + + + - + - Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule. + Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border. KUPO:0001045 kidney proximal convoluted tubule epithelial cell - - - - - true - - Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule. + Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border. FBC:Autogenerated @@ -98864,7 +98994,6 @@ plexiform layer using GABA. - @@ -99132,7 +99261,6 @@ plexiform layer using GABA. - @@ -99147,12 +99275,6 @@ plexiform layer using GABA. glomerular capillary endothelial cell - - - - - true - @@ -99176,7 +99298,7 @@ plexiform layer using GABA. - + @@ -99217,7 +99339,7 @@ plexiform layer using GABA. - + @@ -99229,12 +99351,6 @@ plexiform layer using GABA. KUPO:0001041 kidney efferent arteriole cell - - - - - true - @@ -99423,6 +99539,7 @@ plexiform layer using GABA. + @@ -99435,12 +99552,6 @@ plexiform layer using GABA. kidney cortex artery cell - - - - - true - @@ -99464,6 +99575,7 @@ plexiform layer using GABA. + @@ -99493,7 +99605,6 @@ plexiform layer using GABA. - KUPO:0001096 @@ -99506,7 +99617,6 @@ plexiform layer using GABA. - KUPO:0001098 @@ -99519,7 +99629,6 @@ plexiform layer using GABA. - KUPO:0001100 @@ -99621,12 +99730,6 @@ plexiform layer using GABA. kidney efferent arteriole endothelial cell - - - - - true - @@ -99917,6 +100020,7 @@ plexiform layer using GABA. + @@ -99928,12 +100032,6 @@ plexiform layer using GABA. KUPO:0001067 kidney cortex peritubular capillary cell - - - - - true - @@ -101539,7 +101637,6 @@ plexiform layer using GABA. - @@ -101701,7 +101798,6 @@ plexiform layer using GABA. - @@ -103369,8 +103465,8 @@ plexiform layer using GABA. Any melanocyte that is part of a epidermis. - - 2014-02-03T23:03:09Z + + 2014-02-03T23:03:09Z CL:2000000 These cells are found primarily, but not exclusively, in primates including humans epidermal melanocyte @@ -103407,8 +103503,8 @@ plexiform layer using GABA. A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. - - 2014-02-11T17:29:04Z + + 2014-02-11T17:29:04Z CL:2000001 peripheral blood mononuclear cell @@ -103440,7 +103536,7 @@ plexiform layer using GABA. A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization. - 2014-02-20T23:06:41Z + 2014-02-20T23:06:41Z BTO:0002770 BTO:0005756 NCIT:C32429 @@ -103500,8 +103596,8 @@ plexiform layer using GABA. Any cell that is part of a pituitary gland. - - 2014-03-26T22:14:56Z + + 2014-03-26T22:14:56Z CL:2000004 pituitary gland cell @@ -103537,8 +103633,8 @@ plexiform layer using GABA. Any macroglial cell that is part of a brain. - - 2014-03-28T21:35:27Z + + 2014-03-28T21:35:27Z CL:2000005 brain macroglial cell @@ -103573,8 +103669,8 @@ plexiform layer using GABA. Any germinal center B cell that is part of a tonsil. - - 2014-03-28T21:35:33Z + + 2014-03-28T21:35:33Z CL:2000006 tonsil germinal center B cell @@ -103610,8 +103706,8 @@ plexiform layer using GABA. Chondrocyte forming the hyaline cartilage found in the knee joint. - - 2014-06-04T14:40:11Z + + 2014-06-04T14:40:11Z CL:2000007 articular chondrocyte of knee joint @@ -103646,8 +103742,8 @@ plexiform layer using GABA. Any blood vessel endothelial cell that is part of a microvascular endothelium. - - 2014-06-04T15:07:42Z + + 2014-06-04T15:07:42Z CL:2000008 microvascular endothelial cell @@ -103665,8 +103761,8 @@ plexiform layer using GABA. Any blood vessel endothelial cell that is part of a microvascular endothelium. - - 2014-06-04T15:09:18Z + + 2014-06-04T15:09:18Z CL:2000009 obsolete microvascular endothelium blood vessel endothelial cell true @@ -103702,8 +103798,8 @@ plexiform layer using GABA. Any blood vessel endothelial cell that is part of a dermis. - - 2014-06-04T15:12:06Z + + 2014-06-04T15:12:06Z CL:2000010 dermis blood vessel endothelial cell @@ -103738,8 +103834,8 @@ plexiform layer using GABA. Any endothelial cell of lymphatic vessel that is part of a dermis. - - 2014-06-04T15:15:08Z + + 2014-06-04T15:15:08Z CL:2000011 dermis lymphatic vessel endothelial cell @@ -103774,8 +103870,8 @@ plexiform layer using GABA. Any skin fibroblast that is part of a pedal digit skin. - - 2014-06-04T15:16:44Z + + 2014-06-04T15:16:44Z CL:2000012 fibroblast of pedal digit skin @@ -103810,8 +103906,8 @@ plexiform layer using GABA. Any skin fibroblast that is part of a skin of abdomen. - - 2014-06-04T15:18:16Z + + 2014-06-04T15:18:16Z CL:2000013 fibroblast of skin of abdomen @@ -103846,8 +103942,8 @@ plexiform layer using GABA. Any skin fibroblast that is part of a upper leg skin. - - 2014-06-04T15:19:44Z + + 2014-06-04T15:19:44Z CL:2000014 fibroblast of upper leg skin @@ -103882,8 +103978,8 @@ plexiform layer using GABA. Any skin fibroblast that is part of a arm. - - 2014-06-04T15:29:06Z + + 2014-06-04T15:29:06Z CL:2000015 fibroblast of arm @@ -103913,8 +104009,8 @@ plexiform layer using GABA. Any lung endothelial cell that is part of a microvascular endothelium. - - 2014-06-04T16:00:56Z + + 2014-06-04T16:00:56Z CL:2000016 lung microvascular endothelial cell @@ -103950,8 +104046,8 @@ plexiform layer using GABA. Any fibroblast that is part of a periodontal ligament. - - 2014-06-04T16:50:33Z + + 2014-06-04T16:50:33Z CL:2000017 fibroblast of peridontal ligament @@ -103987,8 +104083,8 @@ plexiform layer using GABA. Any endothelial cell of artery that is part of a coronary artery. - - 2014-06-04T17:08:47Z + + 2014-06-04T17:08:47Z CL:2000018 endothelial cell of coronary artery @@ -104024,8 +104120,8 @@ plexiform layer using GABA. Any photoreceptor cell that is part of a compound eye. - - 2014-06-24T23:16:45Z + + 2014-06-24T23:16:45Z FBbt:00006009 CL:2000019 compound eye photoreceptor cell @@ -104067,8 +104163,8 @@ plexiform layer using GABA. Any native cell that is part of a inner cell mass. - - 2014-06-24T23:16:53Z + + 2014-06-24T23:16:53Z CL:2000020 inner cell mass cell @@ -104103,8 +104199,8 @@ plexiform layer using GABA. Any native cell that is part of a sebaceous gland. - - 2014-06-24T23:17:00Z + + 2014-06-24T23:17:00Z CL:2000021 sebaceous gland cell @@ -104140,8 +104236,8 @@ plexiform layer using GABA. Any native cell that is part of a cardiac septum. - - 2014-06-24T23:17:07Z + + 2014-06-24T23:17:07Z CL:2000022 cardiac septum cell @@ -104176,8 +104272,8 @@ plexiform layer using GABA. Any interneuron that is part of a spinal cord ventral column. - - 2014-06-25T00:23:36Z + + 2014-06-25T00:23:36Z CL:2000023 spinal cord ventral column interneuron @@ -104212,8 +104308,8 @@ plexiform layer using GABA. Any neuron that is part of a spinal cord medial motor column. - - 2014-06-25T00:23:43Z + + 2014-06-25T00:23:43Z CL:2000024 spinal cord medial motor column neuron @@ -104248,8 +104344,8 @@ plexiform layer using GABA. Any oligodendrocyte that is part of a spinal cord. - - 2014-06-25T00:23:50Z + + 2014-06-25T00:23:50Z CL:2000025 spinal cord oligodendrocyte @@ -104266,8 +104362,8 @@ plexiform layer using GABA. Any Golgi cell that is part of a cerebellum. - - 2014-06-25T00:23:57Z + + 2014-06-25T00:23:57Z CL:2000026 obsolete cerebellum Golgi cell true @@ -104299,8 +104395,8 @@ plexiform layer using GABA. Any basket cell that is part of a cerebellum. - - 2014-06-25T00:24:03Z + + 2014-06-25T00:24:03Z CL:2000027 cerebellum basket cell @@ -104330,8 +104426,8 @@ plexiform layer using GABA. Any glutamatergic neuron that is part of a cerebellum. - - 2014-06-25T00:24:10Z + + 2014-06-25T00:24:10Z CL:2000028 cerebellum glutamatergic neuron @@ -104366,8 +104462,8 @@ plexiform layer using GABA. Any neuron that is part of a central nervous system. - - 2014-06-25T01:17:43Z + + 2014-06-25T01:17:43Z CL:2000029 central nervous system neuron @@ -104402,8 +104498,8 @@ plexiform layer using GABA. Any native cell that is part of a hypothalamus. - - 2014-06-25T01:17:50Z + + 2014-06-25T01:17:50Z CL:2000030 hypothalamus cell @@ -104438,8 +104534,8 @@ plexiform layer using GABA. Any neuron that is part of a lateral line ganglion. - - 2014-06-25T01:17:57Z + + 2014-06-25T01:17:57Z CL:2000031 lateral line ganglion neuron @@ -104475,8 +104571,8 @@ plexiform layer using GABA. A neuron that is part of a peripheral nervous system. - - 2014-06-25T02:28:17Z + + 2014-06-25T02:28:17Z FMA:84664 PNS neuron peripheral neuron @@ -104517,8 +104613,8 @@ plexiform layer using GABA. Any basal cell of epidermis that is part of a limb. - - 2014-06-25T02:28:25Z + + 2014-06-25T02:28:25Z CL:2000033 limb basal cell of epidermis @@ -104553,8 +104649,8 @@ plexiform layer using GABA. Any neuromast hair cell that is part of a anterior lateral line. - - 2014-06-25T03:44:37Z + + 2014-06-25T03:44:37Z CL:2000034 anterior lateral line neuromast hair cell @@ -104589,8 +104685,8 @@ plexiform layer using GABA. Any neuromast mantle cell that is part of an anterior lateral line. - - 2014-06-25T03:44:44Z + + 2014-06-25T03:44:44Z CL:2000035 anterior lateral line neuromast mantle cell @@ -104625,8 +104721,8 @@ plexiform layer using GABA. Any neuromast support cell that is part of a anterior lateral line. - - 2014-06-25T03:44:51Z + + 2014-06-25T03:44:51Z anterior lateral line neuromast support cell CL:2000036 anterior lateral line neuromast supporting cell @@ -104662,8 +104758,8 @@ plexiform layer using GABA. Any neuromast hair cell that is part of a posterior lateral line. - - 2014-06-25T03:44:57Z + + 2014-06-25T03:44:57Z CL:2000037 posterior lateral line neuromast hair cell @@ -104698,8 +104794,8 @@ plexiform layer using GABA. Any neuromast mantle cell that is part of a posterior lateral line. - - 2014-06-25T03:45:04Z + + 2014-06-25T03:45:04Z CL:2000038 posterior lateral line neuromast mantle cell @@ -104734,8 +104830,8 @@ plexiform layer using GABA. Any neuromast support cell that is part of a posterior lateral line. - - 2014-06-25T03:45:11Z + + 2014-06-25T03:45:11Z posterior lateral line neuromast support cell CL:2000039 posterior lateral line neuromast supporting cell @@ -104767,8 +104863,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a urinary bladder. - - 2014-07-09T00:04:47Z + + 2014-07-09T00:04:47Z CL:2000040 bladder microvascular endothelial cell @@ -104796,16 +104892,11 @@ plexiform layer using GABA. + - - - - - - Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium. - - 2014-07-09T00:09:54Z + + 2014-07-09T00:09:54Z CL:2000041 dermis microvascular lymphatic vessel endothelial cell @@ -104841,8 +104932,8 @@ plexiform layer using GABA. Any fibroblast that is part of a embryo. - - 2014-07-09T00:12:00Z + + 2014-07-09T00:12:00Z CL:2000042 embryonic fibroblast @@ -104878,8 +104969,8 @@ plexiform layer using GABA. Any pericyte cell that is part of a brain. - - 2014-07-09T00:18:22Z + + 2014-07-09T00:18:22Z CL:2000043 brain pericyte @@ -104916,8 +105007,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a brain. - - 2014-07-09T00:24:53Z + + 2014-07-09T00:24:53Z CL:2000044 brain microvascular endothelial cell @@ -104952,9 +105043,9 @@ plexiform layer using GABA. Any melanocyte of skin that is part of a skin of prepuce of penis. + - - 2014-07-09T00:45:07Z + 2014-07-09T00:45:07Z melanocyte of foreskin CL:2000045 foreskin melanocyte @@ -104990,8 +105081,8 @@ plexiform layer using GABA. Any cardiac muscle cell that is part of a cardiac ventricle. - - 2014-08-12T20:50:28Z + + 2014-08-12T20:50:28Z CL:2000046 ventricular cardiac muscle cell @@ -105028,8 +105119,8 @@ plexiform layer using GABA. Any motor neuron that is part of a brainstem. - - 2014-10-02T23:52:53Z + + 2014-10-02T23:52:53Z CL:2000047 brainstem motor neuron @@ -105054,8 +105145,8 @@ plexiform layer using GABA. A lower motor neuron whose soma is located in the anterior horn. Anterior horn motor neurons project from the anterior portion of the grey matter in the spinal cord to some skeletal muscles. - - 2014-10-03T00:26:27Z + + 2014-10-03T00:26:27Z NCIT:C12645 anterior horn cell ventral horn of spinal cord spinal cord motor neuron @@ -105094,8 +105185,8 @@ plexiform layer using GABA. Any pyramidal cell that is part of a primary motor cortex. - - 2014-10-06T17:39:04Z + + 2014-10-06T17:39:04Z CL:2000049 http://www.ncbi.nlm.nih.gov/pubmed/12524689 primary motor cortex pyramidal cell @@ -105113,8 +105204,8 @@ plexiform layer using GABA. Any retinal ganglion cell that is part of a retina. - - 2014-10-06T17:43:59Z + + 2014-10-06T17:43:59Z CL:2000050 http://www.ncbi.nlm.nih.gov/pubmed/2889210 obsolete retina retinal ganglion cell @@ -105151,8 +105242,8 @@ plexiform layer using GABA. Any fibroblast that is part of a spleen. - - 2014-10-06T18:58:47Z + + 2014-10-06T18:58:47Z CL:2000051 splenic fibroblast @@ -105188,8 +105279,8 @@ plexiform layer using GABA. Any endothelial cell of artery that is part of a umbilical cord. - - 2014-10-06T19:01:48Z + + 2014-10-06T19:01:48Z CL:2000052 http://www.sciencellonline.com/site/productInformation.php?keyword=8010 umbilical artery endothelial cell @@ -105226,8 +105317,8 @@ plexiform layer using GABA. Any endothelial cell that is part of a spleen. - - 2014-10-06T19:06:04Z + + 2014-10-06T19:06:04Z CL:2000053 http://www.sciencellonline.com/site/productInformation.php?keyword=5500 @@ -105290,8 +105381,8 @@ plexiform layer using GABA. Any dendritic cell that is part of a liver. - - 2014-10-06T19:16:11Z + + 2014-10-06T19:16:11Z hepatic dendritic cell CL:2000055 @@ -105312,8 +105403,8 @@ plexiform layer using GABA. Any pyramidal cell that is part of a regional part of cerebral cortex. - - 2014-10-06T19:20:41Z + + 2014-10-06T19:20:41Z CL:2000056 Meynert cell @@ -105349,8 +105440,8 @@ plexiform layer using GABA. Any osteoblast that is part of a femur. - - 2014-10-06T19:29:45Z + + 2014-10-06T19:29:45Z CL:2000057 http://www.sciencellonline.com/site/productInformation.php?keyword=4610 femural osteoblast @@ -105386,8 +105477,8 @@ plexiform layer using GABA. Any osteoblast that is part of a skull. - - 2014-10-06T19:48:30Z + + 2014-10-06T19:48:30Z CL:2000058 http://www.sciencellonline.com/site/productInformation.php?keyword=4600 calvarial osteoblast @@ -105423,8 +105514,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a prostate gland. - - 2014-10-07T17:46:27Z + + 2014-10-07T17:46:27Z CL:2000059 http://www.sciencellonline.com/site/productInformation.php?keyword=4400 @@ -105461,8 +105552,8 @@ plexiform layer using GABA. A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua. - - 2014-10-07T17:48:27Z + + 2014-10-07T17:48:27Z BTO:0006119 BTO:0006208 vCTB @@ -105511,8 +105602,8 @@ plexiform layer using GABA. Any mesenchymal stem cell that is part of a placenta. - - 2014-10-07T17:51:11Z + + 2014-10-07T17:51:11Z CL:2000061 http://www.sciencellonline.com/site/productInformation.php?keyword=7140 @@ -105551,8 +105642,8 @@ plexiform layer using GABA. Any capillary endothelial cell that is part of a placenta. - - 2014-10-07T17:55:56Z + + 2014-10-07T17:55:56Z CL:2000062 http://www.ncbi.nlm.nih.gov/books/NBK53245/ @@ -105589,8 +105680,8 @@ plexiform layer using GABA. Any fibroblast that is part of a female gonad. - - 2014-10-07T17:57:42Z + + 2014-10-07T17:57:42Z CL:2000063 http://www.sciencellonline.com/site/productInformation.php?keyword=7330 ovarian fibroblast @@ -105626,8 +105717,8 @@ plexiform layer using GABA. Any epithelial cell that is part of a female gonad. - - 2014-10-07T17:59:13Z + + 2014-10-07T17:59:13Z CL:2000064 http://www.sciencellonline.com/site/productInformation.php?keyword=7310 @@ -105656,7 +105747,7 @@ plexiform layer using GABA. - + @@ -105665,8 +105756,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a female urethra. - - 2014-10-07T18:18:01Z + + 2014-10-07T18:18:01Z CL:2000065 http://www.sciencellonline.com/site/productInformation.php?keyword=7300 ovarian microvascular endothelial cell @@ -105703,8 +105794,8 @@ plexiform layer using GABA. Any fibroblast that is part of a cardiac ventricle. - - 2014-10-07T18:35:38Z + + 2014-10-07T18:35:38Z CL:2000066 http://www.sciencellonline.com/site/productInformation.php?keyword=6310 @@ -105742,8 +105833,8 @@ plexiform layer using GABA. Any fibroblast that is part of a cardiac atrium. - - 2014-10-07T18:36:54Z + + 2014-10-07T18:36:54Z CL:2000067 http://www.sciencellonline.com/site/productInformation.php?keyword=6320 @@ -105780,8 +105871,8 @@ plexiform layer using GABA. Any fibroblast that is part of a pericardium. - - 2014-10-07T18:38:06Z + + 2014-10-07T18:38:06Z CL:2000068 http://www.sciencellonline.com/site/productInformation.php?keyword=6430 pericardium fibroblast @@ -105817,8 +105908,8 @@ plexiform layer using GABA. Any fibroblast that is part of a gallbladder. - - 2014-10-07T18:41:43Z + + 2014-10-07T18:41:43Z CL:2000069 http://www.sciencellonline.com/site/productInformation.php?keyword=5430 gallbladder fibroblast @@ -105854,8 +105945,8 @@ plexiform layer using GABA. Any fibroblast that is part of a optic choroid. - - 2014-10-07T18:50:43Z + + 2014-10-07T18:50:43Z CL:2000070 http://www.sciencellonline.com/site/productInformation.php?keyword=6620 optic choroid fibroblast @@ -105891,8 +105982,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a breast. - - 2014-10-07T19:55:30Z + + 2014-10-07T19:55:30Z CL:2000071 http://www.sciencellonline.com/site/productInformation.php?keyword=7600 mammary microvascular endothelial cell @@ -105929,8 +106020,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a adipose tissue. - - 2014-10-07T22:13:45Z + + 2014-10-07T22:13:45Z CL:2000072 http://www.sciencellonline.com/site/productInformation.php?keyword=7200 adipose microvascular endothelial cell @@ -105966,8 +106057,8 @@ plexiform layer using GABA. Any migratory neural crest cell that is part of a cardiac neural crest. - - 2014-11-05T01:18:43Z + + 2014-11-05T01:18:43Z cardiac neural crest cell CL:2000073 migratory cardiac neural crest cell @@ -106009,8 +106100,8 @@ plexiform layer using GABA. Any leukocyte that is part of a spleen. - - 2014-11-05T01:26:50Z + + 2014-11-05T01:26:50Z CL:2000074 Splenocytes is a vague term that refers to any one of the different white blood cell types in the spleen. This name is seen many references as such and is not explained further, necessitating a need for this terminology. splenocyte @@ -106046,8 +106137,8 @@ plexiform layer using GABA. Any endodermal cell that is part of a anterior visceral endoderm. - - 2014-11-05T01:34:13Z + + 2014-11-05T01:34:13Z CL:2000075 anterior visceral endoderm cell @@ -106082,8 +106173,8 @@ plexiform layer using GABA. Any vein endothelial cell that is part of a hindlimb stylopod. - - 2014-12-02T18:40:47Z + + 2014-12-02T18:40:47Z CL:2000076 hindlimb stylopod vein endothelial cell @@ -106119,8 +106210,8 @@ plexiform layer using GABA. Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major. - - 2014-12-02T18:48:17Z + + 2014-12-02T18:48:17Z CL:2000077 skeletal muscle tissue of pectoralis major striated muscle cell @@ -106155,8 +106246,8 @@ plexiform layer using GABA. Any pericyte cell that is part of a placenta. - - 2014-12-02T18:51:03Z + + 2014-12-02T18:51:03Z CL:2000078 placental pericyte @@ -106191,8 +106282,8 @@ plexiform layer using GABA. Any mesenchymal stem cell of the bone marrow that is part of a femur. - - 2014-12-02T19:07:31Z + + 2014-12-02T19:07:31Z CL:2000079 mesenchymal stem cell of femoral bone marrow @@ -106227,8 +106318,8 @@ plexiform layer using GABA. Any mesenchymal stem cell of adipose tissue that is part of an abdomen. - - 2014-12-02T19:10:34Z + + 2014-12-02T19:10:34Z mesenchymal stem cell of abdominal adipose CL:2000080 mesenchymal stem cell of abdominal adipose tissue @@ -106264,8 +106355,8 @@ plexiform layer using GABA. Any melanocyte of skin that is part of a skin of face. - - 2014-12-02T19:10:40Z + + 2014-12-02T19:10:40Z CL:2000081 melanocyte of skin of face @@ -106284,8 +106375,8 @@ plexiform layer using GABA. OBSOLETE. Any melanocyte of skin that is part of a skin of prepuce of penis. - - 2014-12-02T19:10:45Z + + 2014-12-02T19:10:45Z CL:2000082 Term was merged into foreskin melanocyte CL_2000045 obsolete melanocyte of foreskin @@ -106322,8 +106413,8 @@ plexiform layer using GABA. Any hair follicle dermal papilla cell that is part of a scalp. - - 2014-12-02T19:10:50Z + + 2014-12-02T19:10:50Z CL:2000083 hair follicle dermal papilla cell of scalp @@ -106353,8 +106444,8 @@ plexiform layer using GABA. Any goblet cell that is part of a conjunctiva. - - 2014-12-02T19:28:38Z + + 2014-12-02T19:28:38Z CL:2000084 conjunctiva goblet cell @@ -106390,8 +106481,8 @@ plexiform layer using GABA. Any mononuclear cell that is part of a umbilical cord. - - 2014-12-02T20:14:16Z + + 2014-12-02T20:14:16Z CL:2000085 mononuclear cell of umbilical cord @@ -106427,8 +106518,8 @@ plexiform layer using GABA. Any basket cell that is part of a neocortex. - - 2014-12-24T00:37:19Z + + 2014-12-24T00:37:19Z CL:2000086 neocortex basket cell @@ -106460,8 +106551,8 @@ plexiform layer using GABA. Any basket cell that is part of a dentate gyrus of hippocampal formation. - - 2014-12-24T00:37:24Z + + 2014-12-24T00:37:24Z CL:2000087 dentate gyrus of hippocampal formation basket cell @@ -106498,8 +106589,8 @@ plexiform layer using GABA. Any basket cell that is part of a Ammon's horn. - - 2014-12-24T00:37:30Z + + 2014-12-24T00:37:30Z CL:2000088 Ammon's horn basket cell @@ -106535,8 +106626,8 @@ plexiform layer using GABA. A granule cell that has soma location in the dentate gyrus cell layer of the hippocampal formation and has an elliptical cell body and characteristic cone-shaped tree of spiny apical dendrites. The branches extend throughout the molecular layer and the distal tips of the dendritic tree end just at the hippocampal fissure or at the ventricular surface. The dentate gyrus granule cell is the principal cell type of the dentate gyrus. - - 2015-02-23T05:48:23Z + + 2015-02-23T05:48:23Z dentate gyrus of hippocampal formation granule cell CL:2000089 As far as can be determined, all dentate granule cells appear to project to CA3 and the axon trajectory is partially correlated with the position of the parent cell body. @@ -106576,8 +106667,8 @@ plexiform layer using GABA. Any stellate cell that is part of a dentate gyrus of hippocampal formation. - - 2015-02-23T05:48:40Z + + 2015-02-23T05:48:40Z CL:2000090 dentate gyrus of hippocampal formation stellate cell @@ -106614,8 +106705,8 @@ plexiform layer using GABA. Any microvascular endothelial cell that is part of a endometrial blood vessel. - - 2015-03-31T21:02:36Z + + 2015-03-31T21:02:36Z CL:2000091 endometrial microvascular endothelial cell @@ -106646,8 +106737,8 @@ plexiform layer using GABA. Any keratinocyte that is part of a hair follicle. - - 2015-03-31T21:07:02Z + + 2015-03-31T21:07:02Z CL:2000092 hair follicular keratinocyte @@ -106683,8 +106774,8 @@ plexiform layer using GABA. Any fibroblast of lung that is part of a bronchus. - - 2015-03-31T21:16:22Z + + 2015-03-31T21:16:22Z CL:2000093 bronchus fibroblast of lung @@ -106712,6 +106803,7 @@ plexiform layer using GABA. + @@ -106720,8 +106812,8 @@ plexiform layer using GABA. Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium. - - 2015-03-31T22:25:17Z + + 2015-03-31T22:25:17Z CL:2000094 nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa @@ -106757,8 +106849,8 @@ plexiform layer using GABA. Any hematopoietic stem cell that is part of a umbilical cord blood. - - 2015-05-26T18:58:34Z + + 2015-05-26T18:58:34Z CL:2000095 cord blood hematopoietic stem cell @@ -106794,8 +106886,8 @@ plexiform layer using GABA. Any fibroblast that is part of a reticular layer of dermis. - - 2015-08-11T16:28:16Z + + 2015-08-11T16:28:16Z CL:2000096 fibroblast of the reticular layer of dermis @@ -106831,8 +106923,8 @@ plexiform layer using GABA. Any dopaminergic neuron that is part of a midbrain. - - 2015-12-03T16:42:40Z + + 2015-12-03T16:42:40Z CL:2000097 midbrain dopaminergic neuron @@ -106868,8 +106960,8 @@ plexiform layer using GABA. A ciliated epithelial cell of the esophagus. - - 2019-02-09T16:40:30Z + + 2019-02-09T16:40:30Z CL:3000000 ciliated epithelial cell of esophagus @@ -106895,9 +106987,9 @@ plexiform layer using GABA. A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin and is present throughout pregnancy. + - - 2019-02-18T19:41:20Z + 2019-02-18T19:41:20Z HBC CL:3000001 @@ -106948,8 +107040,8 @@ plexiform layer using GABA. Sympathetic noradrenergic neuron. - - 2019-02-25T19:30:14Z + + 2019-02-25T19:30:14Z CL:3000002 sympathetic noradrenergic neuron @@ -106981,8 +107073,8 @@ plexiform layer using GABA. Sympathetic cholinergic neuron. - - 2019-02-25T19:32:20Z + + 2019-02-25T19:32:20Z CL:3000003 sympathetic cholinergic neuron @@ -107013,8 +107105,8 @@ plexiform layer using GABA. Peripheral sensory neuron. - - 2019-02-25T19:34:33Z + + 2019-02-25T19:34:33Z CL:3000004 peripheral sensory neuron @@ -107424,8 +107516,7 @@ plexiform layer using GABA. - - + @@ -107602,8 +107693,7 @@ plexiform layer using GABA. - - + @@ -107650,8 +107740,7 @@ plexiform layer using GABA. - - + @@ -109068,9 +109157,9 @@ plexiform layer using GABA. - - - + + + A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus musculus) @@ -109078,34 +109167,34 @@ plexiform layer using GABA. vascular leptomeningeal cell (Mmus) - + - + - + - + PMID:30096314 - + PMID:30096314 - + PMID:30096314 @@ -109361,7 +109450,7 @@ plexiform layer using GABA. - + @@ -109373,6 +109462,12 @@ plexiform layer using GABA. CGE interneuron + caudal ganglionic eminence derived GABAergic cortical interneuron + CGE cortical interneuron + CGE interneuron + CGE-derived GABAergic IN + CGE-derived cell + CGE-derived interneuron caudal ganglionic eminence derived interneuron @@ -109380,7 +109475,58 @@ plexiform layer using GABA. An interneuron that is derived from the caudal ganglionic eminence. - DOI:10.1101/2022.10.12.511898 + PMID:20130169 + PMID:37824655 + PMID:37824663 + + + + + CGE interneuron + PMID:37824663 + + + + + + caudal ganglionic eminence derived GABAergic cortical interneuron + PMID:20130169 + + + + + CGE cortical interneuron + PMID:20130169 + + + + + + CGE interneuron + PMID:37824663 + + + + + + CGE-derived GABAergic IN + PMID:27034423 + + + + + + CGE-derived cell + PMID:27034423 + + + + + + CGE-derived interneuron + PMID:20130169 + PMID:37824655 + @@ -109553,38 +109699,25 @@ plexiform layer using GABA. - - - - - - - - - - - - - - - - - - - - - CGE gaba cortical interneuron - A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. + OBSOLETE. A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. + + CGE cortical interneuron - caudal ganglionic eminence derived GABAergic cortical interneuron + caudal ganglionic eminence derived GABAergic interneuron +and caudal ganglionic eminence derived interneuron are the same cell type. +The two must be merged and one needs to be defined as obsolete. +We decided to deprecate the entity with the more specific term and redundant qualities +in the label. See comments in issue 2357. + obsolete caudal ganglionic eminence derived GABAergic cortical interneuron + true - A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. + OBSOLETE. A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. PMID:20130169 @@ -111966,8 +112099,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + + + + + + An alveolar capillary endothelial cell that is located distally to alveolar capillary type 2 endothelial cells. @@ -112015,8 +112153,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + + + + + + An alveolar capillary endothelial cell that is located proximally to alveolar capillary type 1 endothelial cells and in close apposition to alveolar type 1 epithelial cells (also known as type I pneumocytes). @@ -112126,11 +112269,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances matrix fibroblast 2 mesenchymal alveolar niche cell type-2 associated stromal cell + alveolar type 2 fibroblast cell AF2 + AdvF MANC - alveolar type 2 fibroblast cell + alveolar adventitial fibroblast @@ -112149,6 +112294,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances AF2 + + + + AdvF + PMID:33208946 + + @@ -112548,8 +112700,29 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium. + + + + + + + + + + + + + + + + + + + + + + + A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex. 2022-05-10T13:14:00Z epithelial cell of segment 1 of proximal tubule @@ -112560,7 +112733,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium. + A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex. + PMID:23799132 + PMID:23897681 PMID:31249312 @@ -112569,8 +112744,29 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium. + + + + + + + + + + + + + + + + + + + + + + + A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate. 2022-05-10T13:26:13Z epithelial cell of segment 2 of proximal tubule @@ -112580,8 +112776,11 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium. + A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate. + PMID:23799132 + PMID:23897681 PMID:31249312 + PMID:31253652 @@ -112589,19 +112788,43 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium. + + + + + + + + + + + + + + + + + + A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium, which extends from the medullary rays of the renal cortex into the outer medulla. 2022-05-10T13:31:06Z epithelial cell of segment 3 of proximal tubule + The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury. epithelial cell of proximal tubule segment 3 - Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium. + A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium, which extends from the medullary rays of the renal cortex into the outer medulla. + PMID:23799132 + PMID:31249312 + + + + + The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury. PMID:31249312 @@ -113042,7 +113265,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -114921,21 +115144,21 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. https://orcid.org/0000-0002-1425-877X 2023-10-13T11:22:42Z UB cell ureteric bud cell - + - + PMID:9374839 @@ -115201,7 +115424,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -115415,7 +115638,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -115559,6 +115782,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -116938,12 +117162,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - An epithelial cell part of respiratory tract epithelium that is a precursor of a multi-ciliated cell. This cell actively amplifies centrioles, a required step for multiciliogenesis. @@ -117112,12 +117330,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -117843,7 +118055,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -118090,6 +118302,108 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles. + + + 2024-06-07T12:04:57Z + ovarian pregranulosa cell + pregranulosa cell + PG cell + pre-granulosa cell + + + + + A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles. + PMID:17639032 + PMID:32759216 + PMID:33970370 + PMID:38178246 + + + + + ovarian pregranulosa cell + PMID:32759216 + + + + + pregranulosa cell + PMID:17639032 + PMID:32759216 + + + + + PG cell + PMID:32759216 + + + + + + + + + + + + + + + + + A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH). + + + 2024-06-07T12:15:13Z + EFO:0005289 + MGC + mural GC + mural granulosa cell + + + + + A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH). + PMID:27815559 + PMID:33970370 + PMID:34198768 + + + + + MGC + doi:10.1530/REP-16-0500 + + + + + + mural GC + PMID:34198768 + + + + + @@ -118234,8 +118548,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances fetal alveolar pre-type II epithelial cell fetal pre-type 2 pneumocyte fetal pre-type II alveolar epithelial cell + fetal pre-type II pneumocyte According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350). - fetal pre-type II pneumocyte + fetal pre-type II pulmonary alveolar epithelial cell @@ -118843,6 +119158,105 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + L2MN + An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1. + + 2024-04-23T09:31:39Z + layer 2 marginal neuron + L2MN + L2 marginal neuron + + + + + An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1. + PMID:29311847 + PMID:32108571 + + + + + layer 2 marginal neuron + PMID:32108571 + + + + + L2MN + PMID:29311847 + PMID:32108571 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6. + + 2024-04-23T09:37:55Z + Ivy cell + Lamp5-Lhx6 type + Lamp5 Lhx6 neuron + + + + + A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6. + PMID:34004146 + PMID:36007006 + PMID:37824655 + PMID:37824669 + https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ + + + + + Ivy cell + PMID:36007006 + + + + + Lamp5-Lhx6 type + PMID:30382198 + + + + @@ -119290,6 +119704,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -120898,6 +121318,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -122380,6 +122806,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -122638,12 +123070,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -123640,18 +124066,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - - - - - - - @@ -124246,6 +124660,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125236,6 +125656,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -125464,6 +125896,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -125494,6 +125938,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126016,6 +126466,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126802,14 +127258,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - + - + @@ -126827,5 +127283,5 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + diff --git a/cl.obo b/cl.obo index 3484f534a..22e959469 100644 --- a/cl.obo +++ b/cl.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-05-15 +data-version: releases/2024-07-10 subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,22 +89,27 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" -remark: See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ +remark: See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo. ontology: cl +property_value: dc:description "An ontology of cell types." xsd:string +property_value: dc:title "Cell Ontology" xsd:string property_value: has_ontology_root_term CL:0000000 -property_value: http://purl.org/dc/elements/1.1/description "An ontology of cell types." xsd:string -property_value: http://purl.org/dc/elements/1.1/title "Cell Ontology" xsd:string -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9900-7880 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0002-2244-7917 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-8688-6599 +property_value: terms:contributor https://orcid.org/0000-0002-9900-7880 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:license http://creativecommons.org/licenses/by/4.0/ [Term] id: CHEBI:24431 @@ -112,7 +117,9 @@ is_a: BFO:0000040 [Term] id: CHEBI:36080 -is_a: PR:000000001 ! protein +is_a: BFO:0000002 +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity equivalent_to: PR:000000001 ! protein [Term] @@ -123,7 +130,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -131,7 +138,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -200,7 +207,7 @@ name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell @@ -211,14 +218,14 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] id: CL:0000008 name: migratory cranial neural crest cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] -xref: ZFA:0007091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell [Term] @@ -243,7 +250,7 @@ is_a: CL:0000578 ! experimentally modified cell in vitro id: CL:0000011 name: migratory trunk neural crest cell def: "Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007095] -xref: ZFA:0007095 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell [Term] @@ -266,8 +273,8 @@ id: CL:0000014 name: germ line stem cell def: "A stem cell that is the precursor of gametes." [doi:10.1016/j.stem.2012.05.016] synonym: "germline stem cell" EXACT [] -xref: FBbt:00004861 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -xref: ZFA:0005956 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: FBbt:00004861 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: ZFA:0005956 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 {is_inferred="true"} ! stem cell is_a: CL:0000039 ! germ line cell intersection_of: CL:0000039 ! germ line cell @@ -290,7 +297,7 @@ property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/57 id: CL:0000016 name: male germ line stem cell def: "A stem cell that is the precursor of male gametes." [doi:10.1016/j.stem.2012.05.016] -xref: FBbt:00004929 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004929 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000014 ! germ line stem cell is_a: CL:0000015 ! male germ cell @@ -301,10 +308,10 @@ def: "A male germ cell that develops from spermatogonia. The euploid primary spe xref: BTO:0001275 xref: CALOHA:TS-0951 xref: EMAPA:31484 -xref: FBbt:00004936 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004936 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84049 xref: WBbt:0006799 -xref: ZFA:0009005 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000015 ! male germ cell intersection_of: CL:0000015 ! male germ cell @@ -320,10 +327,10 @@ synonym: "nematoblast" EXACT [] xref: BTO:0001274 xref: CALOHA:TS-0950 xref: EMAPA:31486 -xref: FBbt:00004942 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004942 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:72294 xref: WBbt:0006800 -xref: ZFA:0005769 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005769 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000015 ! male germ cell is_a: CL:0000413 ! haploid cell @@ -348,10 +355,10 @@ synonym: "spermatozoon" EXACT [] xref: BTO:0001277 xref: BTO:0002046 xref: CALOHA:TS-0949 -xref: FBbt:00004954 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004954 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67338 xref: WBbt:0006798 -xref: ZFA:0009006 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000408 {is_inferred="true"} ! male gamete relationship: RO:0002202 CL:0000018 ! develops from spermatid @@ -364,10 +371,10 @@ synonym: "spermatogonial cell" EXACT [] xref: BTO:0000958 xref: CALOHA:TS-2193 xref: EMAPA:31482 -xref: FBbt:00004934 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -xref: FBbt:00004935 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004934 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004935 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:72291 -xref: ZFA:0009007 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009007 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000015 ! male germ cell intersection_of: CL:0000015 ! male germ cell intersection_of: bearer_of PATO:0001394 ! diploid @@ -392,7 +399,7 @@ relationship: capable_of GO:0048477 ! oogenesis id: CL:0000022 name: female germ line stem cell def: "A stem cell that is the precursor of female gametes." [doi:10.1016/j.stem.2012.05.016] -xref: FBbt:00004873 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004873 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000014 {is_inferred="true"} ! germ line stem cell is_a: CL:0000021 {is_inferred="true"} ! female germ cell intersection_of: CL:0000021 ! female germ cell @@ -406,11 +413,11 @@ subset: cellxgene_subset synonym: "oogonium" RELATED [] xref: BTO:0000964 xref: CALOHA:TS-0711 -xref: FBbt:00004886 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004886 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:18644 xref: MESH:D009865 xref: WBbt:0006797 -xref: ZFA:0001109 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0001109 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000021 {is_inferred="true"} ! female germ cell is_a: CL:0000255 ! eukaryotic cell @@ -423,7 +430,7 @@ name: oogonial cell def: "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset xref: FMA:83673 -xref: ZFA:0005878 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005878 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000021 {is_inferred="true"} ! female germ cell intersection_of: CL:0000021 ! female germ cell @@ -440,15 +447,15 @@ synonym: "ovum" EXACT [] xref: BTO:0000369 xref: BTO:0003801 xref: CALOHA:TS-2191 -xref: FBbt:00057012 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00057012 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67343 xref: MESH:D010063 -xref: ZFA:0001570 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0001570 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000675 {is_inferred="true"} ! female gamete relationship: participates_in GO:0007143 ! female meiotic nuclear division relationship: RO:0002202 CL:0000023 ! develops from oocyte -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Egg_cell.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Egg_cell.svg" xsd:anyURI [Term] id: CL:0000026 @@ -456,7 +463,7 @@ name: invertebrate nurse cell def: "A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte." [GOC:tfm, PMID:15848391] synonym: "nurse cell" RELATED [] xref: BTO:0000953 -xref: FBbt:00004878 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004878 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 is_a: CL:0000412 ! polyploid cell is_a: CL:4029002 ! germline-derived nurse cell @@ -484,7 +491,7 @@ id: CL:0000029 name: neural crest derived neuron def: "Any neuron that develops from some migratory neural crest cell." [FBC:Autogenerated] synonym: "neuron neural crest derived" EXACT [] -xref: ZFA:0009009 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000540 {is_inferred="true"} ! neuron intersection_of: CL:0000540 ! neuron @@ -495,7 +502,7 @@ relationship: RO:0002202 CL:0002676 ! develops from neural crest derived neurobl id: CL:0000030 name: glioblast subset: cellxgene_subset -xref: ZFA:0009010 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -509,7 +516,7 @@ subset: cellxgene_subset synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 -xref: ZFA:0009011 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata @@ -519,7 +526,7 @@ id: CL:0000032 name: neuroplacodal cell def: "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." [GOC:tfm, ISBN:0618947256] synonym: "neural placode cell" EXACT [] -xref: ZFA:0009012 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009012 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0002321 ! embryonic cell (metazoa) relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell @@ -543,7 +550,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -558,7 +565,7 @@ def: "A stem cell that self-renews as well as give rise to a single mature cell synonym: "unipotent stem cell" EXACT [] synonym: "unipotential stem cell" EXACT [] xref: FMA:70569 -xref: ZFA:0009013 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -591,7 +598,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -639,7 +646,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -651,7 +658,7 @@ def: "A cell that is within the developmental lineage of gametes and is able to comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim subset: ubprop:upper_level -xref: ZFA:0009016 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: capable_of GO:0022414 ! reproductive process @@ -666,7 +673,7 @@ synonym: "colony forming unit monocyte" RELATED [] synonym: "monocyte stem cell" RELATED [] xref: CALOHA:TS-1195 xref: FMA:83553 -xref: ZFA:0009017 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -714,7 +721,7 @@ name: neutrophilic myeloblast def: "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor." [GOC:add, ISBN:0721601464, PMID:12560239, PMID:15514007] comment: These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction. synonym: "neutrophilic granuloblast" RELATED [] -xref: ZFA:0009018 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009018 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000834 ! neutrophil progenitor cell is_a: CL:0000835 {is_inferred="true"} ! myeloblast intersection_of: CL:0000835 ! myeloblast @@ -777,7 +784,7 @@ synonym: "NSC" EXACT [] xref: BTO:0002881 xref: CALOHA:TS-2360 xref: FMA:86684 -xref: ZFA:0009019 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0002319 ! neural cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -791,7 +798,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -814,7 +821,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor @@ -835,7 +842,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -865,7 +872,7 @@ synonym: "early lymphocyte progenitor" RELATED [] synonym: "ELP" RELATED OMO:0003000 [] synonym: "lymphoid stem cell" RELATED [] synonym: "lymphopoietic stem cell" RELATED [] -xref: ZFA:0009023 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009023 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell @@ -880,7 +887,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -905,10 +912,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -924,7 +931,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell @@ -937,7 +944,7 @@ def: "Skeletogenic cell that is typically non-terminally differentiated, secrete synonym: "chrondoplast" EXACT [] xref: BTO:0003607 xref: FMA:66783 -xref: ZFA:0009027 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009027 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell @@ -973,7 +980,7 @@ xref: BTO:0001769 xref: CALOHA:TS-0696 xref: FMA:62999 xref: MESH:D009804 -xref: ZFA:0009029 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009029 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002148 ! dental pulp cell @@ -991,7 +998,7 @@ comment: Legacy def: A cell of ectomesenchymal origin that aids in the formation synonym: "cementum secreting cell" EXACT [] xref: CALOHA:TS-1164 xref: FMA:63002 -xref: ZFA:0009030 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009030 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000062 ! osteoblast is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0005176 ! tooth enamel organ @@ -1007,7 +1014,7 @@ subset: cellxgene_subset xref: BTO:0001593 xref: CALOHA:TS-0720 xref: FMA:66780 -xref: ZFA:0009031 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009031 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell is_a: CL:0011026 ! progenitor cell @@ -1031,7 +1038,7 @@ def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm] subset: cellxgene_subset xref: VHOG:0001532 xref: XAO:0000031 -xref: ZFA:0009032 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009032 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: has_part GO:0005929 ! cilium @@ -1046,7 +1053,7 @@ subset: human_reference_atlas synonym: "ependymocyte" EXACT [] xref: BTO:0001724 xref: FMA:70550 -xref: ZFA:0009033 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009033 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -1062,14 +1069,14 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1078,7 +1085,7 @@ name: ciliated epithelial cell def: "An epithelial cell that has a cilia." [GOC:tfm] subset: cellxgene_subset xref: FMA:70605 -xref: ZFA:0009035 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009035 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000064 ! ciliated cell is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell @@ -1089,7 +1096,7 @@ id: CL:0000068 name: duct epithelial cell def: "An epithelial cell that is part of a duct." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset -xref: ZFA:0009372 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009372 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000058 ! duct @@ -1111,12 +1118,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -1147,7 +1152,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -1156,7 +1161,7 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] @@ -1167,7 +1172,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 -xref: ZFA:0009040 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell @@ -1176,14 +1181,14 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000078 name: peridermal cell -xref: ZFA:0009041 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009041 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell [Term] id: CL:0000079 name: stratified epithelial cell subset: cellxgene_subset -xref: ZFA:0009042 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009042 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell relationship: RO:0002202 CL:0000357 ! develops from stratified epithelial stem cell @@ -1192,7 +1197,7 @@ relationship: RO:0002202 CL:0000357 ! develops from stratified epithelial stem c id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] -xref: ZFA:0009043 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid @@ -1206,7 +1211,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -1219,9 +1224,9 @@ def: "An epithelial cell of the lung." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset synonym: "lung epithelial cell" EXACT [] xref: BTO:0004299 -is_a: CL:0000066 ! epithelial cell +is_a: CL:0002632 ! epithelial cell of lower respiratory tract intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0002048 ! lung +intersection_of: part_of UBERON:0000115 ! lung epithelium relationship: part_of UBERON:0000115 ! lung epithelium [Term] @@ -1231,13 +1236,11 @@ def: "An epithelial cell of the pancreas." [GOC:tfm] synonym: "pancreas epithelial cell" EXACT [] synonym: "pancreatic epithelial cell" EXACT [] xref: BTO:0000028 -xref: ZFA:0009045 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: BFO:0000002 -is_a: CL:0000066 ! epithelial cell +xref: ZFA:0009045 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas -relationship: RO:0002202 CL:0000223 ! develops from endodermal cell [Term] id: CL:0000084 @@ -1258,7 +1261,7 @@ xref: CALOHA:TS-1001 xref: FMA:62870 xref: MESH:D013601 xref: VHOG:0001479 -xref: ZFA:0009046 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009046 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000542 {is_inferred="true"} ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity @@ -1357,7 +1360,7 @@ xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 xref: MESH:D010010 -xref: ZFA:0009047 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell @@ -1401,7 +1404,7 @@ xref: BTO:0000539 xref: BTO:0001026 xref: CALOHA:TS-0422 xref: FMA:62854 -xref: ZFA:0009048 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte @@ -1451,7 +1454,7 @@ synonym: "polymorphonuclear neutrophil" EXACT [] synonym: "polynuclear neutrophilic leucocyte" EXACT [] synonym: "polynuclear neutrophilic leukocyte" EXACT [] xref: BTO:0003473 -xref: ZFA:0009049 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009049 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000234 ! phagocyte is_a: CL:0000775 {is_inferred="true"} ! neutrophil relationship: capable_of GO:0002536 ! respiratory burst involved in inflammatory response @@ -1522,7 +1525,7 @@ def: "A specialized epithelial cell involved in sensory perception. Restricted t comment: The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). synonym: "neuroepithelial cell" BROAD [] xref: BTO:0004301 -xref: ZFA:0009050 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009050 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000066 ! epithelial cell @@ -1535,10 +1538,10 @@ def: "Most generally any neuron which is not motor or sensory. Interneurons may subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0003811 -xref: FBbt:00005125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67313 xref: WBbt:0005113 -xref: ZFA:0009051 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009051 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -1550,10 +1553,10 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "motoneuron" EXACT [] xref: BTO:0000312 -xref: FBbt:00005123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83617 xref: WBbt:0005409 -xref: ZFA:0009052 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000527 ! efferent neuron property_value: RO:0002175 NCBITaxon:9606 @@ -1563,11 +1566,11 @@ name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] subset: human_reference_atlas xref: BTO:0001037 -xref: FBbt:00005124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 xref: MESH:D011984 xref: WBbt:0005759 -xref: ZFA:0009053 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009053 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000526 ! afferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception @@ -1577,7 +1580,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000102 name: polymodal neuron -xref: ZFA:0009054 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009054 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -1587,7 +1590,7 @@ def: "A type of interneuron that has two neurites, usually an axon and a dendrit subset: BDS_subset subset: cellxgene_subset xref: FMA:67282 -xref: ZFA:0009055 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070006 ! cortical bipolar morphology @@ -1599,7 +1602,7 @@ name: multipolar neuron def: "A neuron with three or more neurites, usually an axon and multiple dendrites." [FMA:67287, GOC:tfm] subset: BDS_subset xref: FMA:67287 -xref: ZFA:0009056 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009056 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070026 ! multipolar neuron morphology @@ -1610,7 +1613,7 @@ id: CL:0000105 name: pseudounipolar neuron def: "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma." [FMA:67305, GOC:tfm] xref: FMA:67305 -xref: ZFA:0009057 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -1619,7 +1622,7 @@ name: unipolar neuron def: "Neuron with one neurite that extends from the cell body." [FMA:67278, GOC:nv] subset: BDS_subset xref: FMA:67278 -xref: ZFA:0009058 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009058 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -1627,7 +1630,7 @@ id: CL:0000107 name: autonomic neuron def: "A neuron whose cell body is within an autonomic ganglion." [GOC:tfm] xref: FMA:80121 -xref: ZFA:0009059 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009059 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:2000032 ! peripheral nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002410 ! has soma location autonomic nervous system @@ -1638,11 +1641,11 @@ id: CL:0000108 name: cholinergic neuron def: "A neuron that uses acetylcholine as a vesicular neurotransmitter." [GOC:tfm] xref: BTO:0004902 -xref: FBbt:00007173 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007173 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84796 xref: MESH:D059329 xref: WBbt:0006840 -xref: ZFA:0009060 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -1653,15 +1656,15 @@ relationship: capable_of GO:0014055 ! acetylcholine secretion, neurotransmission id: CL:0000109 name: adrenergic neuron xref: MESH:D059331 -xref: ZFA:0009061 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009061 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033050 ! catecholaminergic neuron [Term] id: CL:0000110 name: peptidergic neuron def: "A neuron that uses neuropeptides as transmitters." [doi:10.1016/B978-012589762-4/50021-9, PMID:23040809] -xref: FBbt:00004101 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -xref: ZFA:0009062 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: FBbt:00004101 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: ZFA:0009062 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron relationship: capable_of GO:0002790 ! peptide secretion @@ -1678,7 +1681,7 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 -xref: ZFA:0009064 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) @@ -1705,23 +1708,24 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: BFO:0000002 is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000116 name: pioneer neuron def: "Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance." [GOC:cvs, GOC:tfm] -xref: FBbt:00005128 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -xref: ZFA:0009066 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: FBbt:00005128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: ZFA:0009066 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) -xref: ZFA:0009067 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009067 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000540 ! neuron relationship: part_of UBERON:0001017 ! central nervous system @@ -1732,14 +1736,14 @@ id: CL:0000118 name: basket cell def: "Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells." [WikipediaVersioned:Basket_cell&oldid=951703880] subset: BDS_subset -xref: ZFA:0009068 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009068 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000104 ! multipolar neuron is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070002 ! basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070002 ! basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0000119 @@ -1751,7 +1755,7 @@ synonym: "cerebellum Golgi cell" EXACT [] synonym: "Golgi cell" EXACT [] synonym: "Golgi neuron" EXACT [] xref: MESH:D000080906 -xref: ZFA:0009069 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009069 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4023057 ! cerebellar inhibitory GABAergic interneuron [Term] @@ -1760,7 +1764,7 @@ name: granule cell def: "A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb." [https://medical-dictionary.thefreedictionary.com/granule+cell] subset: cellxgene_subset xref: BTO:0003393 -xref: ZFA:0009070 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) [Term] @@ -1775,7 +1779,7 @@ synonym: "Purkinje's cell" EXACT [] xref: BTO:0001011 xref: CALOHA:TS-0845 xref: FMA:67969 -xref: ZFA:0009071 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009071 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:0000527 ! efferent neuron is_a: CL:1001611 ! cerebellar neuron @@ -1788,7 +1792,7 @@ def: "A neuron that has dendritic processes radiating from the cell body forming subset: BDS_subset subset: cellxgene_subset xref: BTO:0002316 -xref: ZFA:0009072 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009072 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000104 ! multipolar neuron is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) @@ -1823,9 +1827,9 @@ synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: CALOHA:TS-0415 -xref: FBbt:00005144 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 -xref: ZFA:0009073 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 @@ -1839,7 +1843,7 @@ synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 xref: CALOHA:TS-2027 xref: FMA:54538 -xref: ZFA:0009074 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) @@ -1854,7 +1858,7 @@ synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: CALOHA:TS-0060 xref: FMA:54537 -xref: ZFA:0009075 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009075 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000126 ! macroglial cell property_value: RO:0002175 NCBITaxon:9606 @@ -1870,7 +1874,7 @@ synonym: "OLs" EXACT [PMID:8734446] xref: BTO:0000962 xref: CALOHA:TS-0709 xref: FMA:54540 -xref: ZFA:0009076 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009076 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000126 {is_inferred="true"} ! macroglial cell is_a: CL:4023154 ! myelinating glial cell relationship: part_of UBERON:0001017 ! central nervous system @@ -1893,7 +1897,7 @@ synonym: "microgliocyte" EXACT [http://www.copewithcytokines.de/] xref: BTO:0000078 xref: BTO:0000962 xref: FMA:54539 -xref: ZFA:0009077 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009077 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell is_a: CL:0000878 ! central nervous system macrophage intersection_of: CL:0000125 ! glial cell @@ -1920,7 +1924,7 @@ relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia id: CL:0000131 name: gut endothelial cell subset: cellxgene_subset -xref: ZFA:0009078 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009078 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell relationship: RO:0002202 CL:0000223 ! develops from endodermal cell @@ -1933,9 +1937,8 @@ subset: eye_upper_slim subset: human_reference_atlas xref: CALOHA:TS-0172 xref: FMA:70614 -xref: ZFA:0009079 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009079 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell -is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0001985 ! corneal endothelium relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell property_value: RO:0002175 NCBITaxon:9606 @@ -1945,7 +1948,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -1970,7 +1973,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -2003,7 +2006,7 @@ synonym: "fat cell" EXACT [] xref: BTO:0000443 xref: CALOHA:TS-0012 xref: FMA:63880 -xref: ZFA:0009082 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009082 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell @@ -2020,7 +2023,7 @@ xref: BTO:0002038 xref: CALOHA:TS-1167 xref: FMA:66779 xref: VSAO:0000124 -xref: ZFA:0009083 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0001035 ! bone cell is_a: CL:0002320 ! connective tissue cell @@ -2036,7 +2039,7 @@ synonym: "cartilage cell" EXACT [] xref: BTO:0000249 xref: CALOHA:TS-0138 xref: FMA:66782 -xref: ZFA:0009084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000153 ! glycosaminoglycan secreting cell is_a: CL:0000667 ! collagen secreting cell relationship: RO:0001025 UBERON:0002418 ! located in cartilage tissue @@ -2046,7 +2049,7 @@ relationship: RO:0002202 CL:0000058 ! develops from chondroblast id: CL:0000140 name: odontocyte def: "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." [GO_REF:0000034] -xref: ZFA:0009086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0002320 ! connective tissue cell relationship: produces UBERON:0001751 ! dentine @@ -2059,7 +2062,7 @@ name: cementocyte def: "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth." [ISBN:0781733901] comment: CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def). xref: FMA:63003 -xref: ZFA:0009087 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009087 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000137 ! osteocyte relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: RO:0002202 CL:0000061 ! develops from cementoblast @@ -2096,7 +2099,7 @@ comment: Note change of name; nearly all somatic cells can present antigens to T subset: blood_and_immune_upper_slim subset: cellxgene_subset synonym: "APC" RELATED OMO:0003000 [] -xref: ZFA:0009088 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II @@ -2106,7 +2109,7 @@ relationship: capable_of GO:0002504 ! antigen processing and presentation of pep id: CL:0000146 name: simple columnar epithelial cell subset: human_reference_atlas -xref: ZFA:0009089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -2117,7 +2120,7 @@ def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 -xref: ZFA:0009090 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009090 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -2134,7 +2137,7 @@ xref: CALOHA:TS-0613 xref: FMA:70545 xref: MESH:D008544 xref: VHOG:0001679 -xref: ZFA:0009091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell @@ -2179,7 +2182,7 @@ name: exocrine cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] subset: general_cell_types_upper_slim xref: FMA:16014 -xref: ZFA:0009092 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland @@ -2191,7 +2194,7 @@ name: glycosaminoglycan secreting cell def: "A cell that secretes glycosaminoglycans." [GOC:tfm] synonym: "GAG secreting cell" EXACT [] synonym: "hyaluronic acid secreting cell" NARROW [] -xref: ZFA:0009093 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000327 ! extracellular matrix secreting cell is_a: CL:0000447 ! carbohydrate secreting cell @@ -2262,7 +2265,7 @@ synonym: "chalice cell" EXACT [] xref: BTO:0001540 xref: FMA:13148 xref: http://en.wikipedia.org/wiki/Goblet_cell -xref: ZFA:0009094 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000319 ! mucus secreting cell @@ -2293,7 +2296,7 @@ subset: general_cell_types_upper_slim subset: human_reference_atlas synonym: "endocrinocyte" EXACT [] xref: FMA:83809 -xref: ZFA:0009096 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000164 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! enteroendocrine cell is_a: CL:0000164 {gci_filler="UBERON:0000160", gci_relation="part_of"} ! enteroendocrine cell @@ -2309,7 +2312,7 @@ subset: cellxgene_subset xref: BTO:0003865 xref: FMA:62930 xref: MESH:D019858 -xref: ZFA:0009097 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009097 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000163 ! endocrine cell @@ -2323,9 +2326,9 @@ subset: human_reference_atlas synonym: "neurosecretory cell" RELATED [] synonym: "neurosecretory neuron" RELATED [] xref: BTO:0002691 -xref: FBbt:00005130 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83810 -xref: ZFA:0009098 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009098 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000163 ! endocrine cell is_a: CL:0000527 ! efferent neuron is_a: CL:0000710 ! neurecto-epithelial cell @@ -2341,7 +2344,7 @@ subset: cellxgene_subset synonym: "phaeochromocyte" EXACT [] xref: BTO:0000259 xref: FMA:69263 -xref: ZFA:0009099 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009099 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000568 ! amine precursor uptake and decarboxylation cell @@ -2349,7 +2352,7 @@ is_a: CL:0000568 ! amine precursor uptake and decarboxylation cell id: CL:0000167 name: peptide hormone secreting cell def: "Any secretory cell that is capable of some peptide hormone secretion." [FBC:Autogenerated] -xref: ZFA:0009100 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009100 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0030072 ! peptide hormone secretion @@ -2360,7 +2363,7 @@ id: CL:0000168 name: insulin secreting cell def: "Any secretory cell that is capable of some insulin secretion." [FBC:Autogenerated] xref: BTO:0000783 -xref: ZFA:0009101 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009101 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -2389,7 +2392,7 @@ xref: EV:0200009 xref: FMA:70586 xref: MA:0002419 xref: ncithesaurus:Beta_Cell -xref: ZFA:0009102 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009102 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000168 {is_inferred="true"} ! insulin secreting cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0000164 ! enteroendocrine cell @@ -2405,7 +2408,7 @@ name: glucagon secreting cell def: "A cell that secretes glucagon." [GOC:tfm] synonym: "glucagon-secreting cell" EXACT [] xref: FMA:84045 -xref: ZFA:0009103 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009103 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070091 ! glucagon secretion @@ -2422,7 +2425,7 @@ synonym: "pancreatic alpha cell" EXACT [] xref: BTO:0000990 xref: FMA:70585 xref: MESH:D050416 -xref: ZFA:0009104 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009104 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002067 ! type A enteroendocrine cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0002067 ! type A enteroendocrine cell @@ -2435,7 +2438,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000172 name: somatostatin secreting cell def: "Any secretory cell that is capable of some somatostatin secretion." [FBC:Autogenerated] -xref: ZFA:0009105 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009105 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070253 ! somatostatin secretion @@ -2455,7 +2458,7 @@ synonym: "pancreatic delta cell" EXACT [] synonym: "somatostatin-secreting pancreatic cell" EXACT [] xref: BTO:0000803 xref: FMA:70587 -xref: ZFA:0005743 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005743 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0000502 ! type D enteroendocrine cell @@ -2468,7 +2471,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000174 name: steroid hormone secreting cell def: "Any secretory cell that is capable of some steroid hormone secretion." [FBC:Autogenerated] -xref: ZFA:0009106 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035929 ! steroid hormone secretion @@ -2501,7 +2504,7 @@ relationship: capable_of GO:0045457 ! ecdysteroid secretion id: CL:0000177 name: testosterone secreting cell def: "Any secretory cell that is capable of some testosterone secretion." [FBC:Autogenerated] -xref: ZFA:0009107 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009107 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035936 ! testosterone secretion @@ -2520,7 +2523,7 @@ xref: CALOHA:TS-1150 xref: EMAPA:29655 xref: FMA:72297 xref: MESH:D007985 -xref: ZFA:0009108 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009108 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000177 ! testosterone secreting cell is_a: CL:4030031 ! interstitial cell @@ -2531,7 +2534,7 @@ relationship: RO:0002202 CL:0009091 ! develops from Leydig stem cell id: CL:0000179 name: progesterone secreting cell def: "Any secretory cell that is capable of some progesterone secretion." [FBC:Autogenerated] -xref: ZFA:0009109 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009109 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0042701 ! progesterone secretion @@ -2541,7 +2544,7 @@ relationship: capable_of GO:0042701 ! progesterone secretion id: CL:0000180 name: estradiol secreting cell def: "A steroid hormone secreting cell that secretes estradiol." [https://orcid.org/0000-0001-5208-3432] -xref: ZFA:0009110 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035938 ! estradiol secretion @@ -2565,7 +2568,7 @@ subset: human_reference_atlas xref: BTO:0000575 xref: CALOHA:TS-0454 xref: FMA:14515 -xref: ZFA:0009111 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell is_a: CL:0000417 ! endopolyploid cell @@ -2592,7 +2595,7 @@ synonym: "myoepitheliocyte" EXACT [] xref: BTO:0002309 xref: CALOHA:TS-2379 xref: FMA:67799 -xref: ZFA:0009113 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009113 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000183 ! contractile cell @@ -2618,15 +2621,15 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000188 @@ -2639,7 +2642,7 @@ synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 -xref: ZFA:0009115 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue @@ -2652,7 +2655,7 @@ name: slow muscle cell def: "A muscle cell that develops tension more slowly than a fast-twitch fiber." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset synonym: "slow muscle fiber" RELATED [ISBN:0815316208] -xref: ZFA:0009116 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009116 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008046 ! extrafusal muscle fiber relationship: RO:0002202 CL:0000857 ! develops from slow muscle myoblast @@ -2662,7 +2665,7 @@ name: fast muscle cell def: "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron." [GOC:tfm, ISBN:0323052908] subset: cellxgene_subset synonym: "glycolytic muscle fiber" EXACT [] -xref: ZFA:0009117 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009117 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008046 ! extrafusal muscle fiber relationship: RO:0002202 CL:0000858 ! develops from fast muscle myoblast @@ -2681,7 +2684,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -2712,7 +2715,7 @@ is_obsolete: true id: CL:0000196 name: insect flight muscle cell def: "A muscle cell that is involved in the mechanism of insect flight. This encompasses both, cells that power flight and cells that control flight." [doi:10.2142/biophysics.7.21] -xref: FBbt:00003360 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003360 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0008003 ! somatic muscle myotube [Term] @@ -2735,7 +2738,7 @@ def: "The peripheral receptor for pain. Includes receptors which are sensitive t comment: Editor note: request detection of stimulus involved in sensory perception of pain; add develops_from relationship synonym: "nociceptor" EXACT [] {seeAlso="https://meshb.nlm.nih.gov/record/ui?ui=D009619"} synonym: "nocireceptor" EXACT [] {seeAlso="https://www.thefreedictionary.com/nocireceptor"} -xref: ZFA:0009119 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009119 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell [Term] @@ -2743,7 +2746,7 @@ id: CL:0000199 name: mechanoreceptor cell def: "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." [MESH:D008465] synonym: "mechanoreceptor" RELATED [MP:0000972] -xref: ZFA:0009120 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009120 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050974 ! detection of mechanical stimulus involved in sensory perception @@ -2765,7 +2768,7 @@ alt_id: CL:0000201 def: "A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [MESH:D006198, WikipediaVersioned:Hair_cell&oldid=1045345915] comment: In mammals these cells are located in the organ of Corti. synonym: "auditory receptor cell" RELATED [] -xref: ZFA:0009121 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009121 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000855 ! sensory hair cell relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound @@ -2788,7 +2791,7 @@ is_a: CL:0000006 ! neuronal receptor cell id: CL:0000205 name: thermoreceptor cell def: "A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain." [GOC:tfm, MESH:D013823, MP:0000971] -xref: ZFA:0009123 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell intersection_of: CL:0000006 ! neuronal receptor cell intersection_of: capable_of GO:0050960 ! detection of temperature stimulus involved in thermoception @@ -2798,7 +2801,7 @@ relationship: capable_of GO:0050960 ! detection of temperature stimulus involved id: CL:0000206 name: chemoreceptor cell def: "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood." [MESH:D002628] -xref: ZFA:0009124 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell intersection_of: capable_of GO:0050907 ! detection of chemical stimulus involved in sensory perception @@ -2816,7 +2819,7 @@ xref: BTO:0004185 xref: FMA:67860 xref: MESH:D018034 xref: Wikipedia:Olfactory_receptor_neuron -xref: ZFA:0009125 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000206 ! chemoreceptor cell intersection_of: CL:0000540 ! neuron @@ -2836,7 +2839,7 @@ def: "A specialized cell involved in gustatory sensory perception." [GOC:tfm, IS subset: cellxgene_subset synonym: "taste bud cell" EXACT [] xref: FMA:67910 -xref: ZFA:0009126 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000206 ! chemoreceptor cell is_a: CL:0002076 ! endo-epithelial cell @@ -2851,20 +2854,20 @@ def: "A cell specialized to detect and transduce light." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 -xref: FBbt:00004211 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 -xref: ZFA:0009127 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -2872,7 +2875,7 @@ id: CL:0000212 name: absorptive cell def: "A cell that takes up and metabolizes substances." [CL:CVS] subset: human_reference_atlas -xref: ZFA:0009129 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009129 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell property_value: RO:0002175 NCBITaxon:9606 @@ -2881,7 +2884,7 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] @@ -2890,7 +2893,7 @@ name: synovial cell def: "A cell located in the synovial joint." [] synonym: "synoviocyte" EXACT [] xref: CALOHA:TS-0995 -xref: ZFA:0009131 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009131 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell is_a: CL:0002078 {is_inferred="true"} ! meso-epithelial cell relationship: part_of UBERON:0002217 ! synovial joint @@ -2899,7 +2902,7 @@ relationship: part_of UBERON:0002217 ! synovial joint id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -2911,7 +2914,7 @@ xref: BTO:0001238 xref: CALOHA:TS-0922 xref: FMA:72298 xref: VHOG:0001348 -xref: ZFA:0009133 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009133 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000511 ! androgen binding protein secreting cell is_a: CL:0000630 {is_inferred="true"} ! supporting cell is_a: CL:0002625 ! seminiferous tubule epithelial cell @@ -2921,7 +2924,7 @@ intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis [Term] id: CL:0000217 name: insulating cell -xref: ZFA:0009134 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009134 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] @@ -2933,7 +2936,7 @@ synonym: "peripheral neuroglial cell" BROAD [] synonym: "Schwann cell" BROAD [] xref: CALOHA:TS-0898 xref: FMA:62121 -xref: ZFA:0009135 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009135 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000217 ! insulating cell is_a: CL:0002573 ! Schwann cell is_a: CL:4023154 ! myelinating glial cell @@ -2943,7 +2946,7 @@ relationship: RO:0002202 CL:0002377 ! develops from immature Schwann cell id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -2964,7 +2967,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -2976,7 +2979,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -2986,7 +2989,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -3123,7 +3126,7 @@ subset: cellxgene_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 -xref: ZFA:0009140 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009140 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000473 ! defensive cell @@ -3146,7 +3149,7 @@ xref: CALOHA:TS-0587 xref: FMA:63261 xref: FMA:83585 xref: MESH:D008264 -xref: ZFA:0009141 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009141 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte @@ -3174,7 +3177,7 @@ xref: CALOHA:TS-0068 xref: FMA:62869 xref: MESH:D001402 xref: VHOG:0001480 -xref: ZFA:0009142 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009142 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity @@ -3197,15 +3200,21 @@ is_a: CL:0000240 ! stratified squamous epithelial cell [Term] id: CL:0000239 name: brush border epithelial cell -xref: ZFA:0009143 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000067 ! ciliated epithelial cell +def: "An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption." [] +comment: All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys. +xref: https://doi.org/10.1152/ajpgi.00005.2011 +xref: PMID:25422372 +xref: ZFA:0009143 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: has_part GO:0005903 ! brush border +relationship: has_part GO:0005903 ! brush border [Term] id: CL:0000240 name: stratified squamous epithelial cell subset: human_reference_atlas -xref: ZFA:0009144 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000079 ! stratified epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -3214,7 +3223,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000241 name: stratified cuboidal epithelial cell subset: human_reference_atlas -xref: ZFA:0009145 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009145 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000079 ! stratified epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -3227,7 +3236,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "Merkel's cell" EXACT [] xref: FMA:70548 -xref: ZFA:0009146 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009146 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0000312 {xref="PMID:19782676"} ! keratinocyte is_a: CL:0000710 ! neurecto-epithelial cell @@ -3248,7 +3257,7 @@ name: transitional epithelial cell def: "A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium." [GOC:tfm, ISBN:0721662544] subset: human_reference_atlas xref: FMA:66778 -xref: ZFA:0009148 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009148 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -3262,7 +3271,7 @@ replaced_by: PO:0000353 [Term] id: CL:0000246 name: Mauthner neuron -xref: ZFA:0009149 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009149 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron [Term] @@ -3275,7 +3284,7 @@ synonym: "Rohon-Beard cell" EXACT [] xref: AAO:0010316 xref: EFO:0003711 xref: VHOG:0001484 -xref: ZFA:0009150 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009150 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000531 ! primary sensory neuron (sensu Teleostei) is_a: CL:4023168 ! somatosensory neuron @@ -3292,7 +3301,7 @@ replaced_by: PO:0020047 [Term] id: CL:0000249 name: hatching gland cell -xref: ZFA:0009151 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009151 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] @@ -3305,7 +3314,7 @@ replaced_by: PO:0020019 [Term] id: CL:0000251 name: extramedullary cell -xref: ZFA:0009152 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009152 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron [Term] @@ -3319,7 +3328,7 @@ replaced_by: PO:0020048 id: CL:0000253 name: eurydendroid cell subset: cellxgene_subset -xref: ZFA:0009153 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009153 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000527 ! efferent neuron [Term] @@ -3548,7 +3557,7 @@ def: "Any photoreceptor cell that is part of some eye." [FBC:Autogenerated] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas -xref: ZFA:0009154 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye @@ -3593,7 +3602,7 @@ replaced_by: PO:0000293 id: CL:0000293 name: structural cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] -xref: ZFA:0005745 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005745 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -3609,7 +3618,7 @@ alt_id: CL:0000471 def: "A peptide hormone secreting cell that produces growth hormone, somatotropin." [GOC:tfm, SANBI:mhl] synonym: "growth hormone secreting cell" EXACT [] synonym: "somatotrophin secreting cell" EXACT [] -xref: ZFA:0009155 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0030252 ! growth hormone secretion @@ -3650,9 +3659,9 @@ def: "A mature sexual reproductive cell having a single set of unpaired chromoso synonym: "haploid germ cell" RELATED [] synonym: "haploid nucleated cell" EXACT [] xref: CALOHA:TS-0395 -xref: FBbt:00005412 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005412 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:18649 -xref: ZFA:0009156 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009156 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000413 ! haploid cell is_a: CL:0000586 {is_inferred="true"} ! germ cell intersection_of: CL:0000586 ! germ cell @@ -3664,7 +3673,7 @@ relationship: capable_of GO:0009566 ! fertilization id: CL:0000301 name: pole cell def: "A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo." [doi:10.1017/CBO9780511818202.015] -xref: FBbt:00000092 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000670 ! primordial germ cell [Term] @@ -3735,7 +3744,7 @@ is_a: CL:0000308 ! metal ion accumulating cell [Term] id: CL:0000311 name: keratin accumulating cell -xref: ZFA:0009157 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009157 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -3751,7 +3760,7 @@ synonym: "malpighian cell" EXACT [] xref: BTO:0000667 xref: CALOHA:TS-0500 xref: FMA:62879 -xref: ZFA:0009158 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009158 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000237 {is_inferred="true"} ! keratinizing barrier epithelial cell is_a: CL:0000362 {is_inferred="true"} ! epidermal cell intersection_of: CL:0000237 ! keratinizing barrier epithelial cell @@ -3817,7 +3826,7 @@ def: "Any secretory cell that is capable of some mucus secretion." [FBC:Autogene subset: cellxgene_subset synonym: "mucous cell" EXACT [] xref: BTO:0003689 -xref: ZFA:0009159 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009159 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000159 ! seromucus secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0070254 ! mucus secretion @@ -3842,14 +3851,16 @@ consider: CL:1001597 [Term] id: CL:0000322 -name: pneumocyte -def: "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." [GOC:tfm, PMID:20054144] +name: pulmonary alveolar epithelial cell +def: "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." [GOC:tfm, PMID:20054144, PMID:29463737] subset: cellxgene_subset synonym: "alveolar epithelial cell" EXACT [] +synonym: "pneumocyte" EXACT [PMID:32491474] synonym: "pneumonocyte" EXACT [] xref: BTO:0000395 xref: CALOHA:TS-2168 xref: FMA:62499 +is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0010003 ! epithelial cell of alveolus of lung relationship: part_of UBERON:0004821 ! pulmonary alveolus epithelium @@ -3880,14 +3891,14 @@ is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000327 name: extracellular matrix secreting cell -xref: ZFA:0009162 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000499 ! stromal cell [Term] id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -3920,7 +3931,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -3938,7 +3949,7 @@ is_a: CL:0000521 ! fungal cell id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -3948,7 +3959,7 @@ alt_id: CL:1000422 def: "A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation." [GOC:tfm, http://www.britannica.com/EBchecked/topic/6405/adrenal-gland] synonym: "medullary chromaffin cell of adrenal gland" EXACT [FMA:69262] xref: FMA:69262 -xref: ZFA:0009167 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009167 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000457 ! biogenic amine secreting cell is_a: CL:1000426 ! chromaffin cell of adrenal gland intersection_of: CL:0000166 ! chromaffin cell @@ -3961,7 +3972,7 @@ id: CL:0000338 name: neuroblast (sensu Nematoda and Protostomia) def: "A neural precursor of the central nervous system." [PMID:1295739] synonym: "neuroblast" BROAD [] -xref: FBbt:00005146 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005146 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000047 ! neural stem cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia @@ -3972,7 +3983,7 @@ name: glioblast (sensu Vertebrata) def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] synonym: "spongioblast" EXACT [] xref: FMA:70564 -xref: ZFA:0009169 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000030 ! glioblast is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell @@ -3981,7 +3992,7 @@ is_a: CL:0011026 ! progenitor cell id: CL:0000340 name: glioblast (sensu Nematoda and Protostomia) def: "A precursor of the central nervous system that gives rise to glial cells only." [doi:10.1002/glia.21162] -xref: FBbt:00005145 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005145 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000030 ! glioblast is_a: CL:0000130 ! neuron associated cell (sensu Nematoda and Protostomia) @@ -3995,7 +4006,7 @@ property_value: RO:0002161 NCBITaxon:33511 id: CL:0000342 name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] -xref: ZFA:0009170 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata @@ -4005,7 +4016,7 @@ id: CL:0000343 name: visual pigment cell (sensu Vertebrata) def: "A pigment cell that is capable of detecting light stimulus that is involved in visual perception." [GOC:tfm] xref: FMA:63846 -xref: ZFA:0009171 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009171 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000149 ! visual pigment cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) @@ -4022,7 +4033,7 @@ id: CL:0000345 name: dental papilla cell def: "A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp." [GOC:tfm, ISBN:0721662544] comment: Merge with odontoblast? -xref: ZFA:0009173 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009173 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0008019 ! mesenchymal cell relationship: part_of UBERON:0001763 ! odontogenic papilla @@ -4045,7 +4056,7 @@ id: CL:0000347 name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim -xref: ZFA:0009174 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell @@ -4058,7 +4069,7 @@ id: CL:0000348 name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim -xref: ZFA:0009175 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell @@ -4071,7 +4082,7 @@ id: CL:0000349 name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] subset: general_cell_types_upper_slim -xref: ZFA:0009176 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure @@ -4108,7 +4119,7 @@ def: "An undifferentiated cell produced by early cleavages of the fertilized egg synonym: "blastomere" EXACT [] xref: BTO:0001473 xref: FMA:72551 -xref: ZFA:0009177 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009177 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000007 ! early embryonic cell (metazoa) [Term] @@ -4116,7 +4127,7 @@ id: CL:0000354 name: blastemal cell synonym: "blastema cell" EXACT [] xref: ncithesaurus:Blastemal_Cell -xref: ZFA:0009178 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009178 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell [Term] @@ -4125,7 +4136,7 @@ name: multi-potent skeletal muscle stem cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. xref: FMA:86767 -xref: ZFA:0009179 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009179 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell is_a: CL:0000188 ! cell of skeletal muscle intersection_of: CL:0000048 ! multi fate stem cell @@ -4139,7 +4150,7 @@ is_a: CL:0000035 ! single fate stem cell [Term] id: CL:0000357 name: stratified epithelial stem cell -xref: ZFA:0009180 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009180 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000036 ! epithelial fate stem cell [Term] @@ -4159,7 +4170,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "vascular smooth muscle cell" EXACT [] synonym: "VSMC" EXACT [] -xref: ZFA:0009181 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009181 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:4033054 ! perivascular cell intersection_of: CL:0000192 ! smooth muscle cell @@ -4178,7 +4189,7 @@ relationship: part_of UBERON:0000085 ! morula id: CL:0000361 name: gastrula cell def: "A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers." [MESH:D005775] -xref: ZFA:0009182 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009182 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000007 ! early embryonic cell (metazoa) relationship: part_of UBERON:0004734 ! gastrula @@ -4194,7 +4205,7 @@ xref: BTO:0001470 xref: CALOHA:TS-0283 xref: FMA:62411 xref: MESH:D000078404 -xref: ZFA:0009183 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009183 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0007376 ! outer epithelium @@ -4272,14 +4283,14 @@ id: CL:0000372 name: tormogen cell def: "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell." [ISBN:978-0801481253] synonym: "socket cell" BROAD [ISBN:978-0801481253] -xref: FBbt:00005171 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005171 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000463 ! epidermal cell (sensu Arthropoda) [Term] id: CL:0000373 name: histoblast def: "A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis." [doi:10.1016/j.cub.2022.01.045] -xref: FBbt:00001789 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001789 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta @@ -4290,7 +4301,7 @@ name: trichogen cell def: "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell." [ISBN:978-0801481253] synonym: "hair cell" BROAD [] xref: BTO:0004744 -xref: FBbt:00005169 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000463 ! epidermal cell (sensu Arthropoda) [Term] @@ -4319,7 +4330,7 @@ is_a: CL:0000630 ! supporting cell [Term] id: CL:0000379 name: sensory processing neuron -xref: ZFA:0009185 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009185 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -4327,7 +4338,7 @@ id: CL:0000380 name: thecogen cell def: "The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron." [Fbbt:00005173] synonym: "fly sheath cell" EXACT [] -xref: FBbt:00005173 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005173 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) [Term] @@ -4343,14 +4354,14 @@ id: CL:0000382 name: scolopale cell def: "A cell that is part of a scolopidium and surrounds the dendrite of a scolopidial neuron." [doi:10.1016/B978-012369493-5.50012-2, doi:10.1017/CBO9780511818202.024] synonym: "scolopidial sheath cell" EXACT [ISBN:978-087969828-7] -xref: FBbt:00005219 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) relationship: part_of UBERON:0001038 ! chordotonal organ [Term] id: CL:0000383 name: nephrogenic mesenchyme stem cell -xref: ZFA:0009187 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009187 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell @@ -4358,14 +4369,14 @@ relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000384 name: ligament cell -xref: ZFA:0009188 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009188 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell [Term] id: CL:0000385 name: prohemocyte (sensu Nematoda and Protostomia) def: "A precursor of mature hemocytes." [doi:10.1016/B978-012369493-5.50008-0] -xref: FBbt:00005062 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005062 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0008001 ! hematopoietic precursor cell property_value: RO:0002161 NCBITaxon:33511 @@ -4378,7 +4389,7 @@ is_a: CL:0000630 ! supporting cell id: CL:0000387 name: hemocyte (sensu Arthropoda) def: "A blood cell of the circulatory system of arthropods." [doi:10.1016/B978-012369493-5.50008-0] -xref: FBbt:00005063 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005063 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000390 ! blood cell (sensu Nematoda and Protostomia) @@ -4392,7 +4403,7 @@ def: "An elongated fibrocyte that is part of a tendon. The cytoplasm is stretche subset: cellxgene_subset synonym: "muscle attachment cell" EXACT [] synonym: "tenocyte" RELATED [] -xref: ZFA:0009189 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009189 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000135 {is_inferred="true"} ! fibrocyte is_a: CL:0000386 ! attachment cell intersection_of: CL:0000135 ! fibrocyte @@ -4430,7 +4441,7 @@ relationship: RO:0002202 CL:0000395 ! develops from procrystal cell id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -4439,7 +4450,7 @@ name: plasmatocyte def: "A phagocytic hemocyte, responsible for the engulfment of small particles, microbes, and apoptotic tissue debris. It may also secretes antimicrobial peptides and contribute to the production and secretion of proteins of the hemolymph." [https://doi.org/10.1016/B978-012369493-5.50008-0] subset: cellxgene_subset synonym: "macrophage" RELATED [] -xref: FBbt:00001685 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001685 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000387 ! hemocyte (sensu Arthropoda) relationship: capable_of GO:0035010 ! encapsulation of foreign target @@ -4447,14 +4458,14 @@ relationship: capable_of GO:0035010 ! encapsulation of foreign target id: CL:0000395 name: procrystal cell def: "A precursor of mature crystal cells." [doi:10.1016/B978-012369493-5.50008-0] -xref: FBbt:00001689 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001689 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000385 ! prohemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000396 name: lamellocyte def: "A hemocyte found in immuno-stimulated larvae." [doi:10.1016/B978-012369493-5.50008-0] -xref: FBbt:00001687 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001687 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000387 ! hemocyte (sensu Arthropoda) [Term] @@ -4502,7 +4513,7 @@ name: CNS interneuron def: "An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. subset: human_reference_atlas -xref: ZFA:0009191 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009191 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000099 ! interneuron @@ -4513,7 +4524,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -4526,14 +4537,14 @@ is_obsolete: true [Term] id: CL:0000406 name: CNS short range interneuron -xref: ZFA:0009194 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009194 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000402 ! CNS interneuron [Term] id: CL:0000407 name: scolopidial ligament cell def: "A cell that anchors the cell body of a scolopidial neuron to the integument." [doi:10.1016/B978-0-12-408088-1.00002-6, doi:10.1023/a\:1018564904170] -xref: FBbt:00005221 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005221 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) relationship: part_of UBERON:0001038 ! chordotonal organ @@ -4559,7 +4570,7 @@ replaced_by: CL:0000382 [Term] id: CL:0000410 name: CNS long range interneuron -xref: ZFA:0009195 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009195 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000402 ! CNS interneuron [Term] @@ -4569,7 +4580,7 @@ def: "An epithelial cell of the hypodermis of Caenorhabditis." [GOC:tfm, http:// comment: This term was originally added to CL for parity with the Worm anatomy ontology, which is dedicated to C elegans. It is not clear if it makes sense to try and generalize the concept and include in CL, and this term may be obsoleted in future. Note there is no similarity to the hypodermis in vertebrates. synonym: "roundworm hypodermal cell" BROAD [] xref: WBbt:0007846 -xref: ZFA:0009196 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009196 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000228 ! multinucleate cell relationship: RO:0002162 NCBITaxon:6237 ! in taxon Caenorhabditis @@ -4690,7 +4701,7 @@ is_a: CL:0002320 ! connective tissue cell [Term] id: CL:0000428 name: yolk cell -xref: ZFA:0000084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0000084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000349 ! extraembryonic cell @@ -4699,7 +4710,7 @@ id: CL:0000429 name: imaginal disc cell def: "A columnar epithelial cell that is part of an insect imaginal disc." [doi:10.1007/s00412-016-0595-4] comment: This term does not encompass all the cell types that may be found in an epithelial disc (such as the peripodial or adepithelial cells), only the cells that form the disc epithelium proper. -xref: FBbt:00007108 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007108 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000146 ! simple columnar epithelial cell is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000939 ! imaginal disc @@ -4710,7 +4721,7 @@ id: CL:0000430 name: xanthophore cell def: "A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red." [SANBI:mhl] synonym: "xanthophore" RELATED [] -xref: ZFA:0009198 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009198 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell relationship: RO:0002202 CL:0005002 ! develops from xanthoblast @@ -4720,7 +4731,7 @@ id: CL:0000431 name: iridophore def: "A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color." [SANBI:mhl] synonym: "guanophore" RELATED [] -xref: ZFA:0009199 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009199 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell relationship: RO:0002202 CL:0005001 ! develops from iridoblast @@ -4733,7 +4744,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "reticulum cell" EXACT [] xref: FMA:62877 -xref: ZFA:0009200 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000057 ! fibroblast property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string @@ -4756,7 +4767,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000435 name: alkali secreting cell -xref: ZFA:0009201 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009201 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] @@ -4778,7 +4789,7 @@ synonym: "gonadotropic cell" EXACT [] synonym: "pituitary delta cell" EXACT [] xref: BTO:0002482 xref: FMA:83100 -xref: ZFA:0009202 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009202 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000438 ! luteinizing hormone secreting cell is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis @@ -4786,7 +4797,7 @@ is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis id: CL:0000438 name: luteinizing hormone secreting cell def: "A peptide hormone secreting cell pituitary that produces luteinizing hormone." [GOC:tfm] -xref: ZFA:0009203 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009203 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0032275 ! luteinizing hormone secretion @@ -4796,7 +4807,7 @@ relationship: capable_of GO:0032275 ! luteinizing hormone secretion id: CL:0000439 name: prolactin secreting cell def: "A peptide hormone cell that secretes prolactin." [GOC:tfm, SANBI:mhl] -xref: ZFA:0009204 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009204 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell @@ -4810,7 +4821,7 @@ def: "A cell of the intermediate pituitary that produces melanocyte stimulating synonym: "melanotrope" EXACT [] synonym: "melanotroph" EXACT [] xref: BTO:0002277 -xref: ZFA:0009205 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009205 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0036160 ! melanocyte-stimulating hormone secretion @@ -4821,7 +4832,7 @@ id: CL:0000441 name: follicle stem cell (sensu Arthropoda) def: "A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods." [doi:10.1016/B978-012369493-5.50005-5, doi:10.1038/s41467-020-19361-0, doi:10.1242/dev.121.11.3797] synonym: "somatic stem cell" BROAD [doi:10.1016/j.devcel.2005.08.012] -xref: FBbt:00004903 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004903 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000036 ! epithelial fate stem cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:6656 {IAO:0000233="https://github.com/obophenotype/cell-ontology/issues/1943"} ! only in taxon Arthropoda @@ -4843,7 +4854,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000443 name: calcitonin secreting cell def: "Any secretory cell that is capable of some calcitonin secretion." [FBC:Autogenerated] -xref: ZFA:0009206 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009206 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0036161 ! calcitonin secretion @@ -4921,7 +4932,7 @@ xref: BTO:0002042 xref: CALOHA:TS-0194 xref: FMA:83036 xref: MESH:D003713 -xref: ZFA:0009209 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell intersection_of: CL:0000738 ! leukocyte @@ -4950,7 +4961,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000452 name: thyroid hormone secreting cell -xref: ZFA:0009210 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009210 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000163 ! endocrine cell [Term] @@ -4981,7 +4992,7 @@ name: epinephrine secreting cell def: "A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types." [GOC:tfm, PMID:12438093] synonym: "adrenaline secreting cell" EXACT [GO:0048242] synonym: "epinephrin secreting cell" EXACT [] -xref: ZFA:0009211 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0048242 ! epinephrine secretion @@ -5006,7 +5017,7 @@ relationship: capable_of GO:0035931 ! mineralocorticoid secretion [Term] id: CL:0000457 name: biogenic amine secreting cell -xref: ZFA:0009212 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009212 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] @@ -5015,7 +5026,7 @@ name: serotonin secreting cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] -xref: ZFA:0009213 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001820 ! serotonin secretion @@ -5028,7 +5039,7 @@ def: "A cell capable of producting norepiniphrine. Norepiniphrine is a catechola synonym: "noradrenaline secreting cell" EXACT [] synonym: "norepinephrin secreting cell" EXACT [] synonym: "norepinephrine secreting cell" EXACT [] -xref: ZFA:0009214 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009214 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0048243 ! norepinephrine secretion @@ -5038,7 +5049,7 @@ relationship: capable_of GO:0048243 ! norepinephrine secretion id: CL:0000460 name: glucocorticoid secreting cell def: "Any secretory cell that is capable of some glucocorticoid secretion." [FBC:Autogenerated] -xref: ZFA:0009215 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009215 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035933 ! glucocorticoid secretion @@ -5048,7 +5059,7 @@ relationship: capable_of GO:0035933 ! glucocorticoid secretion id: CL:0000462 name: adepithelial cell def: "A cell of mesodermal origin that is closely associated with the epithelium of an imaginal disc. It is a precursor of some of the insect's adult muscles." [doi:10.1016/S0925-4773(97)00654-0] -xref: FBbt:00003219 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000680 ! muscle precursor cell relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta @@ -5058,7 +5069,7 @@ id: CL:0000463 name: epidermal cell (sensu Arthropoda) def: "An epidermal cell that secretes chitinous cuticle from its apical side." [FlyBase:ds, ISBN:ISBN\:978-0801481253] comment: While insect epidermis is generally columnar/cuboidal, there are certainly well studied cases where it is not (e.g.- Rhodnius prolixus when starved). So it would be safer to add this as a differentium for particular species where this is known. -DSJ. -xref: FBbt:00007325 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000362 ! epidermal cell is_a: CL:0000710 ! neurecto-epithelial cell @@ -5069,7 +5080,7 @@ relationship: RO:0002202 CL:0000464 ! develops from epidermoblast id: CL:0000464 name: epidermoblast def: "An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions." [GOC:tfm, PMID:7576311] -xref: FBbt:00004994 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004994 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell @@ -5078,7 +5089,7 @@ relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell id: CL:0000465 name: cardioblast (sensu Arthropoda) def: "A precursor of the cells that form the dorsal vessel of arthropods." [doi:10.1007/BF00360522] -xref: FBbt:00001666 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001666 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010021 ! cardiac myoblast relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda @@ -5093,7 +5104,7 @@ synonym: "adrenocorticotrophic hormone secreting cell" EXACT [] synonym: "corticotrophin hormone secreting cell" EXACT [] synonym: "corticotropin hormone secreting cell" EXACT [] synonym: "corticotropin secreting cell" EXACT [GO:0051458] -xref: ZFA:0009216 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009216 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0051458 ! corticotropin secretion @@ -5105,7 +5116,7 @@ name: neuroglioblast (sensu Nematoda and Protostomia) def: "A precursor of the central nervous system that gives rise to both neurons and glial cells." [doi:10.1002/glia.21162] synonym: "neuro-glioblast" EXACT [] synonym: "neuroglioblast" EXACT [] -xref: FBbt:00005147 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005147 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000047 ! neural stem cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia @@ -5114,7 +5125,7 @@ relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia id: CL:0000469 name: ganglion mother cell def: "A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells." [] -xref: FBbt:00005149 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005149 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 is_a: CL:0011020 ! neural progenitor cell relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda and Protostomia) @@ -5122,7 +5133,7 @@ relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda a [Term] id: CL:0000470 name: digestive enzyme secreting cell -xref: ZFA:0009217 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009217 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell [Term] @@ -5143,7 +5154,7 @@ id: CL:0000474 name: pericardial nephrocyte def: "An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel." [FBbt:00003184, GO:0061320, GOC:tfm, PMID:19783135] synonym: "pericardial cell" NARROW [FBbt:00005058, GO:0061320] -xref: FBbt:00005058 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005058 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) is_a: CL:0002520 ! nephrocyte @@ -5163,7 +5174,7 @@ synonym: "thyroid stimulating hormone secreting cell" EXACT [] synonym: "thyrotrope" EXACT [] xref: FMA:83099 xref: MESH:D052684 -xref: ZFA:0009218 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009218 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis relationship: capable_of GO:0070460 ! thyroid-stimulating hormone secretion @@ -5173,7 +5184,7 @@ name: follicle cell of egg chamber def: "A somatic epithelial cell of the insect egg chamber." [] synonym: "follicle cell" BROAD [] synonym: "ovarian follicle cell" BROAD [] -xref: FBbt:00004904 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004904 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000500 ! follicular epithelial cell @@ -5209,7 +5220,7 @@ is_a: CL:0000167 ! peptide hormone secreting cell id: CL:0000482 name: juvenile hormone secreting cell def: "An endocrine cell that secretes juvenile hormone." [GO:tfm] -xref: FBbt:00058020 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00058020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0045443 ! juvenile hormone secretion @@ -5259,7 +5270,7 @@ name: garland cell def: "A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae." [fbbt:00005059, GOC:tfm, PMID:19783135] synonym: "garland nephrocyte" BROAD [GO:0061321] xref: BTO:0004596 -xref: FBbt:00005059 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005059 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000227 ! binucleate cell is_a: CL:0000519 ! phagocyte (sensu Nematoda and Protostomia) is_a: CL:0002520 ! nephrocyte @@ -5269,7 +5280,7 @@ id: CL:0000487 name: oenocyte def: "A secretory cell of ectodermal origin. This cell may have important functions in fatty acid and hydrocarbon metabolism and is metabolically linked to the fat body and tracheae. This cell is exclusive of arthropods." [GOC:bf, https://www.merriam-webster.com/dictionary/oenocyte, PMID:11171397, PMID:24397521, PMID:34208190] comment: Oenocytes are highly variable in size, shape, cluster formation and anatomical location. In adults, oenocytes tend to be smaller but more numerous than in larvae. While oenocytes have been found in arachnids and crustaceans, they have been most abundantly described in insects. {xref="PMID:34208190", xref="PMID:24397521"} -xref: FBbt:00004995 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004995 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000151 ! secretory cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda @@ -5278,7 +5289,7 @@ relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda id: CL:0000488 name: visible light photoreceptor cell def: "A photoreceptor cell that detects visible light." [GOC:tfm] -xref: ZFA:0009219 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: capable_of GO:0009584 ! detection of visible light @@ -5292,7 +5303,7 @@ is_a: CL:0000210 ! photoreceptor cell [Term] id: CL:0000490 name: photopic photoreceptor cell -xref: ZFA:0009220 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009220 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000488 ! visible light photoreceptor cell [Term] @@ -5333,7 +5344,7 @@ is_obsolete: true id: CL:0000494 name: UV sensitive photoreceptor cell def: "A photoreceptor cell that detects ultraviolet light." [GOC:tfm] -xref: ZFA:0009221 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009221 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: capable_of GO:0009589 ! detection of UV @@ -5343,21 +5354,21 @@ relationship: capable_of GO:0009589 ! detection of UV id: CL:0000495 name: blue sensitive photoreceptor cell def: "A photoreceptor cell that is sensitive to blue light." [GO:tfm] -xref: ZFA:0009222 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009222 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000490 ! photopic photoreceptor cell [Term] id: CL:0000496 name: green sensitive photoreceptor cell def: "A photoreceptor cell that is sensitive to green light." [GO:tfm] -xref: ZFA:0009223 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009223 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000490 ! photopic photoreceptor cell [Term] id: CL:0000497 name: red sensitive photoreceptor cell def: "A photoreceptor cell that is sensitive to red light." [GO:tfm] -xref: ZFA:0009224 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009224 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000490 ! photopic photoreceptor cell [Term] @@ -5366,7 +5377,7 @@ name: inhibitory interneuron def: "An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS)." [GOC:tfm, http://en.wikipedia.org/wiki/Interneuron] subset: cellxgene_subset xref: FMA:84776 -xref: ZFA:0009225 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009225 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron [Term] @@ -5378,7 +5389,7 @@ subset: general_cell_types_upper_slim subset: human_reference_atlas xref: BTO:0002064 xref: FMA:83624 -xref: ZFA:0009226 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell @@ -5399,9 +5410,10 @@ synonym: "granulosa cell of ovary" EXACT [] xref: BTO:0000542 xref: CALOHA:TS-0729 xref: FMA:18718 -xref: ZFA:0009227 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009227 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell is_a: CL:0002174 ! follicular cell of ovary +relationship: RO:0002207 CL:4033066 ! directly develops from pre-granulosa cell [Term] id: CL:0000502 @@ -5410,7 +5422,7 @@ def: "A cell found throughout the gastrointestinal tract and in the pancreas. Th subset: cellxgene_subset synonym: "D cell" EXACT [] xref: FMA:62935 -xref: ZFA:0009228 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009228 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000172 ! somatostatin secreting cell @@ -5421,7 +5433,7 @@ def: "A flattened stroma cell forming a sheath or theca outside the basal lamina subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0002850 -xref: ZFA:0009229 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009229 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary relationship: part_of UBERON:0001305 ! ovarian follicle @@ -5441,21 +5453,21 @@ is_a: CL:0002274 ! histamine secreting cell id: CL:0000505 name: substance P secreting cell def: "A peptide hormone secreting cell that secretes substance P." [GO:tfm] -xref: ZFA:0009230 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009230 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell [Term] id: CL:0000506 name: enkephalin secreting cell def: "An endorphine cell that secretes enkephalin." [GO:tfm] -xref: ZFA:0009231 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009231 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000507 ! endorphin secreting cell [Term] id: CL:0000507 name: endorphin secreting cell def: "A peptide hormone secreting cell that secretes endorphin." [GO:tfm] -xref: ZFA:0009232 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009232 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell [Term] @@ -5502,7 +5514,7 @@ is_a: CL:0000154 ! protein secreting cell id: CL:0000512 name: paracrine cell def: "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it." [GOC:tfm, ISBN:0198529171] -xref: ZFA:0009233 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009233 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] @@ -5514,7 +5526,7 @@ subset: cellxgene_subset synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 -xref: ZFA:0009234 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009234 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast intersection_of: CL:0000056 ! myoblast @@ -5530,7 +5542,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -5542,7 +5554,7 @@ name: skeletal muscle myoblast def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 -xref: ZFA:0009236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000056 ! myoblast @@ -5559,7 +5571,7 @@ synonym: "perineural satellite cell" EXACT [] synonym: "perineuronal satellite oligodendroglial cell" EXACT [] synonym: "satellite oligodendrocyte" EXACT [] xref: FMA:54550 -xref: ZFA:0009237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) property_value: RO:0002175 NCBITaxon:9606 @@ -5652,7 +5664,7 @@ def: "A neuron which conveys sensory information centrally from the periphery." subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 -xref: ZFA:0009238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -5661,7 +5673,7 @@ id: CL:0000527 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:D009476] synonym: "output neuron" EXACT [] -xref: ZFA:0009239 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -5669,21 +5681,21 @@ id: CL:0000528 name: nitrergic neuron def: "A nerve cell where transmission is mediated by nitric oxide." [MESH:D026602] xref: FMA:84792 -xref: ZFA:0009240 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009240 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] id: CL:0000529 name: pigmented epithelial cell subset: cellxgene_subset -xref: ZFA:0009241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000710 ! neurecto-epithelial cell [Term] id: CL:0000530 name: primary neuron (sensu Teleostei) def: "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed." [doi:10.1242/dev.108.1.121, PMID:1842357] -xref: ZFA:0009242 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009242 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000540 ! neuron @@ -5702,14 +5714,14 @@ intersection_of: CL:0000530 ! primary neuron (sensu Teleostei) [Term] id: CL:0000532 name: CAP motoneuron -xref: ZFA:0009243 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009243 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000533 ! primary motor neuron (sensu Teleostei) [Term] id: CL:0000533 name: primary motor neuron (sensu Teleostei) def: "A primary neuron (sensu Teleostei) that has a motor function." [PMID:1842357] -xref: ZFA:0009244 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009244 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron is_a: CL:0000530 ! primary neuron (sensu Teleostei) @@ -5717,7 +5729,7 @@ is_a: CL:0000530 ! primary neuron (sensu Teleostei) id: CL:0000534 name: primary interneuron (sensu Teleostei) def: "A primary neuron (sensu Teleostei) that is neither a sensory neuron or a motor neuron." [PMID:1842357] -xref: ZFA:0009245 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009245 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:0000530 ! primary neuron (sensu Teleostei) @@ -5725,7 +5737,7 @@ is_a: CL:0000530 ! primary neuron (sensu Teleostei) id: CL:0000535 name: secondary neuron (sensu Teleostei) def: "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages." [doi:10.1242/dev.108.1.121, PMID:1842357] -xref: ZFA:0009246 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009246 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000540 ! neuron @@ -5735,7 +5747,7 @@ relationship: RO:0002160 NCBITaxon:32443 {IAO:0000233="https://github.com/obophe id: CL:0000536 name: secondary motor neuron (sensu Teleostei) def: "A secondary neuron (sensu Teleostei) that has a motor function." [PMID:1842357] -xref: ZFA:0009247 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009247 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron is_a: CL:0000535 ! secondary neuron (sensu Teleostei) intersection_of: CL:0000100 ! motor neuron @@ -5772,17 +5784,17 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse relationship: RO:0002202 CL:0000031 {gci_filler="NCBITaxon:7742", gci_relation="RO:0002162", xref="https://github.com/obophenotype/cell-ontology/issues/757"} ! develops from neuroblast (sensu Vertebrata) -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -5792,7 +5804,7 @@ def: "A cell that originates from the neural crest and differentiates into a pig comment: Derived from UBERON:0002342 neural crest. xref: BTO:0003217 xref: FMA:83377 -xref: ZFA:0009249 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -5809,7 +5821,7 @@ xref: CALOHA:TS-0583 xref: FMA:62863 xref: MESH:D008214 xref: VHOG:0001535 -xref: ZFA:0009250 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009250 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -5948,7 +5960,7 @@ subset: cellxgene_subset subset: ubprop:upper_level synonym: "metazoan cell" EXACT [] relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2124 -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Animal_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Animal_cells.svg" xsd:anyURI is_obsolete: true replaced_by: CL:0000000 @@ -5961,7 +5973,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -5982,7 +5994,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -6117,7 +6129,7 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] -xref: ZFA:0009251 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell @@ -6149,7 +6161,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -6189,7 +6201,7 @@ subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0004657 xref: FMA:83551 -xref: ZFA:0009253 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -6211,7 +6223,7 @@ synonym: "band cell" BROAD [] synonym: "band form" BROAD [] synonym: "rod neutrophil" EXACT [] synonym: "stab cell" BROAD [] -xref: ZFA:0009254 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009254 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000096 {is_inferred="true"} ! mature neutrophil intersection_of: CL:0000096 ! mature neutrophil intersection_of: CL:4030045 PR:000009978 ! lacks_part lactotransferrin @@ -6247,7 +6259,7 @@ synonym: "ACs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "amacrine neuron" EXACT [] xref: BTO:0004044 xref: FMA:67766 -xref: ZFA:0009255 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009255 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell @@ -6262,7 +6274,7 @@ name: nucleate erythrocyte def: "An erythrocyte having a nucleus." [GOC:add, GOc:tfm] synonym: "RBC" BROAD [] synonym: "red blood cell" BROAD [] -xref: ZFA:0009256 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009256 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000232 {is_inferred="true"} ! erythrocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000232 ! erythrocyte @@ -6285,7 +6297,7 @@ comment: These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-pos synonym: "neutrophilic premyelocyte" EXACT [] synonym: "neutrophilic progranulocyte" EXACT [] xref: FMA:84196 -xref: ZFA:0009257 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009257 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000834 ! neutrophil progenitor cell is_a: CL:0000836 {is_inferred="true"} ! promyelocyte intersection_of: CL:0000836 ! promyelocyte @@ -6317,7 +6329,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -6349,7 +6361,7 @@ id: CL:0000569 name: cardiac mesenchymal cell def: "A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field." [PMID:18816864] subset: cellxgene_subset -xref: ZFA:0009259 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009259 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell is_a: CL:2000073 ! migratory cardiac neural crest cell intersection_of: CL:0008019 ! mesenchymal cell @@ -6367,7 +6379,7 @@ synonym: "parafollicular cell of thyroid gland" EXACT [FMA:68653] synonym: "thyroid parafollicular cell" EXACT [FMA:68653] xref: FMA:68653 xref: SCTID:176770005 -xref: ZFA:0009260 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009260 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000443 {is_inferred="true"} ! calcitonin secreting cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000710 {is_inferred="true"} ! neurecto-epithelial cell @@ -6385,7 +6397,7 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0000571 name: leucophore def: "A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light." [SANBI:mhl] -xref: ZFA:0009261 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009261 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell relationship: RO:0002202 CL:0005003 ! develops from leucoblast @@ -6400,7 +6412,7 @@ synonym: "cone" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 -xref: ZFA:0009262 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009262 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -6409,7 +6421,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000574 name: erythrophore def: "A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance." [SANBI:mhl] -xref: ZFA:0009263 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009263 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell relationship: RO:0002202 CL:0005004 ! develops from pigment erythroblast @@ -6426,7 +6438,7 @@ synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: CALOHA:TS-0173 xref: FMA:70551 -xref: ZFA:0009264 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009264 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell @@ -6446,7 +6458,7 @@ subset: human_reference_atlas xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 -xref: ZFA:0009265 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009265 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0011026 ! progenitor cell @@ -6493,7 +6505,7 @@ is_a: CL:0001034 ! cell in vitro id: CL:0000579 name: border follicle cell def: "A follicle cell that migrates from the anterior pole of the insect egg chamber to the anterior of the oocyte where they participate in the formation of the micropyle." [FBbt:00004905] -xref: FBbt:00004905 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004905 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000477 ! follicle cell of egg chamber [Term] @@ -6503,7 +6515,7 @@ def: "A neutrophil precursor in the granulocytic series, being a cell intermedia comment: These cells are also CD15-positive, CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. xref: BTO:0003455 xref: FMA:83540 -xref: ZFA:0009266 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009266 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000776 {is_inferred="true"} ! immature neutrophil is_a: CL:0002087 ! nongranular leukocyte is_a: CL:0002193 ! myelocyte @@ -6545,7 +6557,7 @@ def: "A macrophage resident in the peritoneum under non-inflammatory conditions. comment: Markers: Mouse: F4/80-high, CD11b-high, CD68+, SIGNR1+, Dectin-1+. xref: BTO:0001034 xref: FMA:83025 -xref: ZFA:0009267 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009267 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0042742 ! defense response to bacterium @@ -6574,7 +6586,7 @@ def: "A neutrophil precursor in the granulocytic series, being a cell intermedia comment: These cells are also CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction. synonym: "juvenile neutrophil" EXACT [] xref: FMA:84197 -xref: ZFA:0009268 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009268 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000776 {is_inferred="true"} ! immature neutrophil is_a: CL:0002192 ! metamyelocyte intersection_of: CL:0000776 ! immature neutrophil @@ -6662,7 +6674,7 @@ synonym: "mature enterocyte" NARROW [https://orcid.org/0000-0001-9610-7627, PMID xref: BTO:0000398 xref: FMA:62122 xref: MESH:D020895 -xref: ZFA:0009269 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009269 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0000677 ! gut absorptive cell is_a: CL:0002563 ! intestinal epithelial cell @@ -6699,7 +6711,7 @@ name: odontoclast def: "A specialized osteoclast associated with the absorption and removal of cementum." [GOC:add] xref: BTO:0002516 xref: FMA:83027 -xref: ZFA:0009270 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009270 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000092 {is_inferred="true"} ! osteoclast intersection_of: CL:0000092 ! osteoclast intersection_of: capable_of GO:0042483 ! negative regulation of odontogenesis @@ -6746,7 +6758,7 @@ relationship: RO:0002202 CL:0000501 ! develops from granulosa cell id: CL:0000593 name: androgen secreting cell def: "A steroid hormone secreting cell that secretes androgen." [GOC:tfm] -xref: ZFA:0009271 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009271 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0035935 ! androgen secretion @@ -6758,7 +6770,7 @@ name: skeletal muscle satellite cell def: "An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers." [GOC:tfm, MESH:D032496, PMID:21849021, PMID:23303905] comment: Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population. subset: cellxgene_subset -xref: ZFA:0009272 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009272 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0000680 ! muscle precursor cell @@ -6802,7 +6814,7 @@ xref: BTO:0003102 xref: FMA:67310 xref: FMA:86775 xref: NIFSTD:sao862606388 -xref: ZFA:0009273 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009273 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000104 ! multipolar neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070015 ! pyramidal family morphology @@ -6835,7 +6847,7 @@ is_a: CL:4023120 ! cochlea auditory hair cell id: CL:0000602 name: pressoreceptor cell def: "A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls." [MESH:D011311] -xref: ZFA:0009274 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009274 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000082 ! stretch receptor cell [Term] @@ -6855,7 +6867,7 @@ synonym: "rod" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 -xref: ZFA:0009275 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009275 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -7085,11 +7097,11 @@ name: GABAergic neuron def: "A neuron that uses GABA as a vesicular neurotransmitter" [GOC:tfm] subset: cellxgene_subset synonym: "GABA-ergic neuron" EXACT [] -xref: FBbt:00007228 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007228 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84788 xref: MESH:D059330 xref: WBbt:0005190 -xref: ZFA:0009276 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -7129,7 +7141,7 @@ synonym: "acinic cell" EXACT [] synonym: "acinous cell" EXACT [] xref: FMA:83625 xref: MESH:D061354 -xref: ZFA:0009277 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000154 ! protein secreting cell relationship: part_of UBERON:0009842 ! glandular acinus @@ -7151,7 +7163,7 @@ xref: FMA:63147 xref: FMA:83601 xref: MESH:D007694 xref: VHOG:0001697 -xref: ZFA:0009278 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001067 ! group 1 innate lymphoid cell intersection_of: CL:0001067 ! group 1 innate lymphoid cell intersection_of: capable_of GO:0002228 ! natural killer cell mediated immunity @@ -7208,7 +7220,7 @@ name: olfactory granule cell def: "A granule cell that has a soma located in an olfactory bulb granule cell layer. An olfactory granule cell is an interneuron that lacks an axon, makes reciprocal dendro-dendritic synapses with mitral cells and tufted cells and is involved in the fine spatio-temporal tuning of the responses of these principal olfactory bulb neurons to odors." [doi:10.1038/s41598-018-27692-8, GOC:mah] comment: Granule cells are the most abundant neuronal population in the olfactory bulb and are continuously renewed throughout life. {xref="doi:10.1038/s41598-018-27692-8"} synonym: "olfactory bulb granule cell" EXACT [doi:10.1038/s41598-018-27692-8] -xref: ZFA:0001694 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0001694 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000120 ! granule cell is_a: CL:0012001 ! neuron of the forebrain is_a: CL:1001434 ! olfactory bulb interneuron @@ -7248,7 +7260,7 @@ def: "A cell whose primary function is to support other cell types." [FB:ma, GOC subset: cellxgene_subset synonym: "supportive cell" EXACT [] xref: BTO:0002315 -xref: ZFA:0009387 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009387 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -7273,7 +7285,7 @@ synonym: "vitamin A-storing cells" RELATED [PMID:12808230] xref: BTO:0002741 xref: CALOHA:TS-0452 xref: FMA:67763 -xref: ZFA:0009279 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009279 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000057 ! fibroblast is_a: CL:0000327 ! extracellular matrix secreting cell intersection_of: CL:0002320 ! connective tissue cell @@ -7322,7 +7334,7 @@ synonym: "Muller cell" EXACT MISSPELLING [doi:10.21769/BioProtoc.4179] synonym: "Muller glia" EXACT [] synonym: "Müller cell" EXACT [] xref: BTO:0003064 -xref: ZFA:0009280 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009280 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000681 ! radial glial cell is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -7381,7 +7393,7 @@ synonym: "FS cell" RELATED OMO:0003000 [PMID:34734454] synonym: "FSC" RELATED OMO:0003000 [doi:10.23937/2572-407X.1510006] synonym: "pituitary folliculostellate cell" EXACT [PMID:34734454] synonym: "Sox2-positive stem cell" RELATED [PMID:34734454] -xref: ZFA:0009281 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009281 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000512 ! paracrine cell is_a: CL:0000630 ! supporting cell is_a: CL:2000004 ! pituitary gland cell @@ -7396,7 +7408,7 @@ subset: human_reference_atlas synonym: "Bergmann astrocyte" EXACT [] synonym: "Bergmann glial cell of cerebellum" EXACT [] xref: FMA:54559 -xref: ZFA:0009282 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009282 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000127 ! astrocyte property_value: RO:0002175 NCBITaxon:9606 @@ -7455,7 +7467,7 @@ synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] xref: FMA:84138 -xref: ZFA:0005238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000192 ! smooth muscle cell is_a: CL:1000618 ! juxtaglomerular complex cell @@ -7489,7 +7501,7 @@ xref: BTO:0000853 xref: CALOHA:TS-0617 xref: FMA:70972 xref: MESH:D050527 -xref: ZFA:0009283 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009283 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000669 ! pericyte relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell @@ -7509,7 +7521,7 @@ name: pinealocyte def: "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation." [GOC:tfm, http://en.wikipedia.org/wiki/Pinealocyte, ISBN:0517223651, PMID:16687276] xref: BTO:0001068 xref: FMA:83417 -xref: ZFA:0009284 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009284 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000163 ! endocrine cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002319 ! neural cell @@ -7529,7 +7541,7 @@ synonym: "kidney podocyte" EXACT [] synonym: "renal podocyte" EXACT [] xref: BTO:0002295 xref: FMA:70967 -xref: ZFA:0009285 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009285 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002522 ! renal filtration cell is_a: CL:1000450 ! epithelial cell of glomerular capsule intersection_of: CL:0000066 ! epithelial cell @@ -7586,7 +7598,7 @@ name: secondary spermatocyte def: "One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids." [GOC:tfm, ISBN:0721662544] xref: BTO:0000709 xref: CALOHA:TS-2195 -xref: FBbt:00004941 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004941 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:72293 is_a: CL:0000017 ! spermatocyte is_a: CL:0000413 ! haploid cell @@ -7649,18 +7661,22 @@ replaced_by: CL:1000147 [Term] id: CL:0000666 -name: fenestrated cell +name: fenestrated endothelial cell +def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset synonym: "window cell" EXACT [] -xref: ZFA:0009286 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000066 ! epithelial cell +xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000115 ! endothelial cell +intersection_of: CL:0000115 ! endothelial cell +intersection_of: bearer_of PATO:0002064 ! fenestrated +relationship: bearer_of PATO:0002064 ! fenestrated [Term] id: CL:0000667 name: collagen secreting cell def: "An extracellular matrix secreting cell that secretes collagen." [GOC:tfm] subset: cellxgene_subset -xref: ZFA:0009287 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009287 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000327 ! extracellular matrix secreting cell [Term] @@ -7688,7 +7704,7 @@ synonym: "pericyte cell" EXACT [] synonym: "pericyte of Rouget" EXACT [] xref: BTO:0002441 xref: FMA:63174 -xref: ZFA:0009112 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009112 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell @@ -7703,7 +7719,7 @@ subset: cellxgene_subset synonym: "gonocyte" EXACT [] synonym: "primitive germ cell" EXACT [] xref: FMA:70567 -xref: ZFA:0009288 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009288 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000039 {is_inferred="true"} ! germ line cell is_a: CL:0000219 {is_inferred="true"} ! motile cell intersection_of: CL:0000039 ! germ line cell @@ -7716,7 +7732,7 @@ id: CL:0000671 name: centripetally migrating follicle cell def: "A follicle cell that migrates from the dorso-anterior part of the oocyte associated follicular epithelium, in between the nurse cells and the oocyte, and participates in the formation of the operculum." [PMID:36807509] synonym: "centripetal follicle cell" EXACT [] -xref: FBbt:00004906 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004906 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000477 ! follicle cell of egg chamber [Term] @@ -7732,7 +7748,7 @@ name: Kenyon cell def: "An intrinsic neuron of the mushroom body of arthropods and annelids. They have tightly packed, cytoplasm-poor cell bodies." [doi:10.1016/S1467-8039(03)00009-4] synonym: "globuli cell" RELATED [] synonym: "mushroom body intrinsic neuron" BROAD [] -xref: FBbt:00003686 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003686 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000028 ! CNS neuron (sensu Nematoda and Protostomia) relationship: part_of UBERON:0001058 ! mushroom body @@ -7742,7 +7758,7 @@ name: interfollicle cell def: "A follicle cell that is part of the stalk connecting adjacent egg chambers." [PMID:36531940] synonym: "stalk cell" EXACT [] synonym: "stalk follicle cell" EXACT [] -xref: FBbt:00004910 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004910 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000477 ! follicle cell of egg chamber [Term] @@ -7763,7 +7779,7 @@ id: CL:0000677 name: gut absorptive cell def: "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." [JB:jb] subset: cellxgene_subset -xref: ZFA:0009289 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009289 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: part_of UBERON:0001277 ! intestinal epithelium @@ -7778,9 +7794,9 @@ name: glutamatergic neuron def: "A neuron that is capable of some neurotansmission by glutamate secretion." [] subset: cellxgene_subset subset: human_reference_atlas -xref: FBbt:00100291 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006829 -xref: ZFA:0009290 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009290 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -7793,7 +7809,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell @@ -7808,7 +7824,7 @@ def: "A cell present in the developing CNS. Functions as both a precursor cell a comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life. subset: cellxgene_subset synonym: "forebrain radial glial cell" NARROW [] -xref: ZFA:0009292 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009292 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell relationship: RO:0002202 CL:0000710 ! develops from neurecto-epithelial cell @@ -7824,7 +7840,7 @@ synonym: "M-cell" EXACT [] synonym: "microfold cell" EXACT [] xref: BTO:0003600 xref: FMA:62929 -xref: ZFA:0009293 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009293 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000473 ! defensive cell is_a: CL:0000627 ! transporting cell is_a: CL:0002251 ! epithelial cell of alimentary canal @@ -7837,7 +7853,7 @@ name: ependymoglial cell def: "A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space." [http://neurolex.org/wiki/Category\:Ependymoglial_Cell, JB:jb] synonym: "ependymal astrocyte" EXACT [] xref: MESH:D063928 -xref: ZFA:0009294 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009294 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000127 ! astrocyte [Term] @@ -7857,7 +7873,7 @@ replaced_by: PO:0004010 id: CL:0000686 name: cerebrospinal fluid secreting cell def: "A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid." [GOC:tfm] -xref: ZFA:0009295 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009295 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 {is_inferred="true"} ! secretory cell is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000151 ! secretory cell @@ -7869,7 +7885,7 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0000687 name: R1 photoreceptor cell synonym: "R1 cell" EXACT [] -xref: FBbt:00004213 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -7878,7 +7894,7 @@ relationship: part_of UBERON:0000971 ! ommatidium id: CL:0000688 name: perijunctional fibroblast def: "A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina." [JB:jb] -xref: ZFA:0009296 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009296 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000057 ! fibroblast is_a: CL:0000630 ! supporting cell @@ -7892,7 +7908,7 @@ is_a: CL:0000163 ! endocrine cell id: CL:0000690 name: R2 photoreceptor cell synonym: "R2 cell" EXACT [] -xref: FBbt:00004215 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004215 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -7902,7 +7918,7 @@ id: CL:0000691 name: stellate interneuron def: "Any interneuron that has characteristic some stellate morphology." [FBC:Autogenerated] subset: BDS_subset -xref: ZFA:0009297 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009297 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:0000104 ! multipolar neuron intersection_of: CL:0000099 ! interneuron @@ -7917,7 +7933,7 @@ synonym: "perisynaptic Schwann cell" EXACT [PMID:18803315] synonym: "Schwann cell" BROAD [] synonym: "teloglia" EXACT [PMID:18803315] synonym: "tSC" RELATED OMO:0003000 [PMID:18803315] -xref: ZFA:0009298 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009298 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell is_a: CL:0002376 ! non-myelinating Schwann cell @@ -7929,7 +7945,7 @@ subset: BDS_subset synonym: "neuroglioform cell" EXACT [PMID:3235828] synonym: "NGF cell" EXACT [PMID:18568015] synonym: "spiderweb cell" EXACT [] -xref: ZFA:0009299 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009299 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:0000104 ! multipolar neuron intersection_of: CL:0000099 ! interneuron @@ -7940,7 +7956,7 @@ relationship: bearer_of PATO:0070001 ! neurogliaform morphology id: CL:0000694 name: R3 photoreceptor cell synonym: "R3 cell" EXACT [] -xref: FBbt:00004217 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004217 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -7953,12 +7969,12 @@ comment: While previously called 'pioneer neurons' of the marginal zone, Cajal-R subset: cellxgene_subset synonym: "CR cells" EXACT [WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753] synonym: "Horizontal cells of Cajal" EXACT [WikipediaVersioned:Cajal–Retzius_cell&oldid=1032081753] -xref: ZFA:0009300 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009300 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron relationship: bearer_of PATO:0070006 ! cortical bipolar morphology relationship: RO:0002100 UBERON:0010403 ! has soma location brain marginal zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:0000696 @@ -7975,7 +7991,7 @@ is_a: CL:0000167 ! peptide hormone secreting cell id: CL:0000697 name: R4 photoreceptor cell synonym: "R4 cell" EXACT [] -xref: FBbt:00004219 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -7998,11 +8014,11 @@ def: "A neuron that releases dopamine as a neurotransmitter." [GOC:dhill] subset: cellxgene_subset synonym: "dopaminergic cell" EXACT [] xref: BTO:0004032 -xref: FBbt:00005131 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005131 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84787 xref: MESH:D059290 xref: WBbt:0006746 -xref: ZFA:0009301 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009301 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033050 ! catecholaminergic neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061527 ! dopamine secretion, neurotransmission @@ -8018,7 +8034,7 @@ is_a: CL:0000630 ! supporting cell id: CL:0000702 name: R5 photoreceptor cell synonym: "R5 cell" EXACT [] -xref: FBbt:00004221 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004221 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -8028,7 +8044,7 @@ id: CL:0000703 name: sustentacular cell def: "Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors." [JB:jb] xref: BTO:0002315 -xref: ZFA:0009302 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009302 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell [Term] @@ -8036,14 +8052,14 @@ id: CL:0000704 name: endothelial tip cell def: "A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels." [PMID:15376331] subset: cellxgene_subset -xref: ZFA:0009303 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009303 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000071 ! blood vessel endothelial cell [Term] id: CL:0000705 name: R6 photoreceptor cell synonym: "R6 cell" EXACT [] -xref: FBbt:00004223 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004223 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -8058,21 +8074,21 @@ subset: human_reference_atlas synonym: "choroid plexus cell" BROAD [DOI:10.1101/2022.10.12.511898] synonym: "epithelial cell of choroid plexus" EXACT [] xref: FMA:70549 -xref: ZFA:0009304 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009304 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000065 ! ependymal cell is_a: CL:0000627 ! transporting cell is_a: CL:0002319 ! neural cell intersection_of: CL:0000065 ! ependymal cell intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: part_of UBERON:0001886 ! choroid plexus -property_value: http://purl.org/dc/terms/date "2023-08-04T08:48:30Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2023-08-04T08:48:30Z" xsd:dateTime [Term] id: CL:0000707 name: R7 photoreceptor cell synonym: "R7 cell" EXACT [] -xref: FBbt:00004225 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004225 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000494 ! UV sensitive photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -8083,7 +8099,7 @@ name: leptomeningeal cell def: "Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus." [JB:jb] subset: cellxgene_subset synonym: "leptomemingeal cell" RELATED [] -xref: ZFA:0009305 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009305 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000327 {is_inferred="true"} ! extracellular matrix secreting cell is_a: CL:0002319 ! neural cell intersection_of: CL:0000327 ! extracellular matrix secreting cell @@ -8094,7 +8110,7 @@ relationship: part_of UBERON:0003210 ! blood-cerebrospinal fluid barrier id: CL:0000709 name: R8 photoreceptor cell synonym: "R8 cell" EXACT [] -xref: FBbt:00004227 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004227 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000488 ! visible light photoreceptor cell is_a: CL:2000019 ! compound eye photoreceptor cell relationship: part_of UBERON:0000971 ! ommatidium @@ -8143,7 +8159,7 @@ is_a: CL:0000711 ! cumulus cell id: CL:0000715 name: embryonic crystal cell def: "A crystal cell that derives from the embryonic head mesoderm." [] -xref: FBbt:00001690 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001690 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000392 ! crystal cell is_a: CL:0011008 ! embryonic hemocyte @@ -8170,7 +8186,7 @@ def: "A cell of an ommatidium that secretes lens materials." [doi:10.1017/CBO978 comment: Not to be confused with the Semper cells of the Semper organ found in gastropods. {xref="doi:10.1242/jcs.s3-105.71.331"} synonym: "cone cell (sensu Endopterygota)" RELATED [] synonym: "Semper cell" EXACT [] -xref: FBbt:00004193 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000306 ! crystallin accumulating cell is_a: CL:0002319 ! neural cell relationship: part_of UBERON:0000971 ! ommatidium @@ -8203,7 +8219,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -8267,7 +8283,7 @@ def: "A cell of a layer of transitional epithelium in the wall of the proximal u subset: cellxgene_subset synonym: "urinary tract transitional epithelial cell" NARROW [] xref: FMA:84127 -xref: ZFA:0009308 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009308 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000244 ! transitional epithelial cell intersection_of: CL:0000244 ! transitional epithelial cell intersection_of: part_of UBERON:0000365 ! urothelium @@ -8296,12 +8312,12 @@ replaced_by: CL:0011009 id: CL:0000735 name: lymph gland hemocyte def: "A hemocyte that derives from the larval lymph gland." [doi:10.1242/dev.00702] -xref: FBbt:00005917 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005917 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000387 ! hemocyte (sensu Arthropoda) [Term] id: CL:0000736 -name: embryonic gland hemocyte +name: obsolete embryonic gland hemocyte comment: Obsoleted as this term probably resulted from a confusion. Hemocytes are either derived from the embryonic head mesoderm ("embryonic hemocytes") or from the larval lymph gland ("lymph gland hemocytes"), not from an "embryonic gland". is_obsolete: true replaced_by: CL:0011008 @@ -8313,7 +8329,7 @@ def: "Muscle cell which has as its direct parts myofilaments organized into sarc xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 -xref: ZFA:0005784 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005784 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0001410 ! striated @@ -8336,7 +8352,7 @@ xref: CALOHA:TS-0549 xref: FMA:62852 xref: MESH:D007962 xref: NCIT:C12529 -xref: ZFA:0009309 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009309 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell @@ -8365,7 +8381,7 @@ synonym: "RGCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 -xref: ZFA:0009310 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009310 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) relationship: RO:0002100 UBERON:0000966 ! has soma location retina property_value: RO:0002175 NCBITaxon:9606 @@ -8375,14 +8391,14 @@ id: CL:0000741 name: spinal accessory motor neuron def: "A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord." [PMID:16267219] synonym: "SACMN" EXACT [] -xref: ZFA:0009311 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009311 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008039 ! lower motor neuron [Term] id: CL:0000742 name: periarticular chondrocyte def: "A round chondrocyte that first differentiates in the late embryonic growth plate of bone." [PMID:15951842] -xref: ZFA:0009312 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009312 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1001607 ! articular chondrocyte [Term] @@ -8391,7 +8407,7 @@ name: hypertrophic chondrocyte def: "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." [GO_REF:0000034, PMID:15951842] comment: is hypertrophic pathological or normal? and can it be described using a pato term? subset: human_reference_atlas -xref: ZFA:0009313 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000138 ! chondrocyte property_value: RO:0002175 NCBITaxon:9606 @@ -8399,7 +8415,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000744 name: columnar chondrocyte def: "A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate." [PMID:15951842] -xref: ZFA:0009314 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000138 ! chondrocyte [Term] @@ -8413,7 +8429,7 @@ synonym: "HC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] xref: BTO:0004120 -xref: ZFA:0009315 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron relationship: RO:0002100 UBERON:0003902 ! has soma location retinal neural layer property_value: RO:0002175 NCBITaxon:9606 @@ -8436,7 +8452,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 xref: MESH:D032383 -xref: ZFA:0009316 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000737 ! striated muscle cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000187 ! muscle cell @@ -8454,7 +8470,7 @@ id: CL:0000747 name: cyanophore def: "A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance." [SANBI:mhl] synonym: "blue chromatophore" RELATED [] -xref: ZFA:0009317 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell relationship: RO:0002202 CL:0005005 ! develops from cyanoblast @@ -8469,7 +8485,7 @@ subset: human_reference_atlas synonym: "BC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "BCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "BPs" RELATED OMO:0003004 [GSE137537] -xref: ZFA:0009318 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009318 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000103 ! bipolar neuron is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0008028 ! visual system neuron @@ -8485,7 +8501,7 @@ name: ON-bipolar cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors." [PMID:14689473] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009319 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009319 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000748 ! retinal bipolar neuron property_value: RO:0002175 NCBITaxon:9606 @@ -8495,7 +8511,7 @@ name: OFF-bipolar cell def: "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolarize in response to light to dark transition." [PMID:14689473] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009320 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009320 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000748 ! retinal bipolar neuron property_value: RO:0002175 NCBITaxon:9606 @@ -8506,7 +8522,7 @@ def: "A bipolar neuron found in the retina that is synapsed by rod photoreceptor subset: cellxgene_subset subset: human_reference_atlas xref: FMA:67750 -xref: ZFA:0009321 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009321 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000749 ! ON-bipolar cell @@ -8520,7 +8536,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000752 name: cone retinal bipolar cell def: "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer." [PMID:14689473] -xref: ZFA:0009322 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000748 ! retinal bipolar neuron intersection_of: CL:0000748 ! retinal bipolar neuron intersection_of: RO:0002103 CL:0000573 ! synapsed by retinal cone cell @@ -8616,7 +8632,7 @@ name: nucleated thrombocyte def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. subset: blood_and_immune_upper_slim -xref: ZFA:0009323 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell intersection_of: CL:0000763 ! myeloid cell @@ -8633,7 +8649,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell @@ -8652,7 +8668,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -8667,7 +8683,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -8706,7 +8722,7 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009326 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte @@ -8900,7 +8916,7 @@ xref: BTO:0000130 xref: CALOHA:TS-0688 xref: FMA:62860 xref: MESH:D009504 -xref: ZFA:0009327 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009327 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II @@ -8919,7 +8935,7 @@ synonym: "immature neutrocyte" EXACT [] synonym: "immature neutrophil leucocyte" EXACT [] synonym: "immature neutrophil leukocyte" EXACT [] synonym: "immature neutrophilic leucocyte" EXACT [] -xref: ZFA:0009328 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009328 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000775 {is_inferred="true"} ! neutrophil intersection_of: CL:0000775 ! neutrophil intersection_of: has_part CL:0017509 ! alobate nucleus @@ -8944,7 +8960,7 @@ id: CL:0000778 name: mononuclear osteoclast def: "A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts." [GOC:add, GOC:tfm, PMID:12713016, PMID:15055519, PMID:17380158, PMID:9415452] comment: Morphology: mononuclear, highly vesicular. -xref: ZFA:0009329 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009329 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000092 {is_inferred="true"} ! osteoclast is_a: CL:0000113 ! mononuclear phagocyte intersection_of: CL:0000092 ! osteoclast @@ -8979,7 +8995,7 @@ id: CL:0000781 name: mononuclear odontoclast def: "A specialized mononuclear osteoclast associated with the absorption and removal of cementum." [GOC:add, PMID:9415452] comment: Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth. -xref: ZFA:0009330 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000588 {is_inferred="true"} ! odontoclast is_a: CL:0000778 {is_inferred="true"} ! mononuclear osteoclast intersection_of: CL:0000588 ! odontoclast @@ -9045,7 +9061,7 @@ subset: cellxgene_subset synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] -xref: ZFA:0009331 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009331 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive @@ -9076,7 +9092,7 @@ synonym: "plasmocyte" EXACT [] xref: BTO:0000392 xref: FMA:70574 xref: MESH:D010950 -xref: ZFA:0009332 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex @@ -9104,7 +9120,7 @@ subset: human_reference_atlas synonym: "memory B lymphocyte" EXACT [] synonym: "memory B-cell" EXACT [] synonym: "memory B-lymphocyte" EXACT [] -xref: ZFA:0009333 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009333 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000785 {is_inferred="true"} ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: CL:4030046 PR:000001935 ! lacks_plasma_membrane_part syndecan-1 @@ -9127,7 +9143,7 @@ subset: human_reference_atlas synonym: "naive B lymphocyte" EXACT [] synonym: "naive B-cell" EXACT [] synonym: "naive B-lymphocyte" EXACT [] -xref: ZFA:0009334 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009334 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000785 {is_inferred="true"} ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: CL:4030044 GO:0002344 ! has_not_completed B cell affinity maturation @@ -9151,7 +9167,7 @@ subset: cellxgene_subset synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] -xref: ZFA:0009335 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex @@ -9327,7 +9343,7 @@ synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] -xref: ZFA:0009336 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -9342,7 +9358,7 @@ comment: Note that gamma-delta T cells have both thymic and extrathymic differen synonym: "immature gamma-delta T lymphocyte" EXACT [] synonym: "immature gamma-delta T-cell" EXACT [] synonym: "immature gamma-delta T-lymphocyte" EXACT [] -xref: ZFA:0009337 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009337 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000798 {is_inferred="true"} ! gamma-delta T cell is_a: CL:0002420 ! immature T cell intersection_of: CL:0000798 ! gamma-delta T cell @@ -9359,7 +9375,7 @@ subset: cellxgene_subset synonym: "mature gamma-delta T lymphocyte" EXACT [] synonym: "mature gamma-delta T-cell" EXACT [] synonym: "mature gamma-delta T-lymphocyte" EXACT [] -xref: ZFA:0009338 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009338 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000798 {is_inferred="true"} ! gamma-delta T cell is_a: CL:0002419 ! mature T cell intersection_of: CL:0000798 ! gamma-delta T cell @@ -9375,7 +9391,7 @@ synonym: "gamma-delta intraepithelial T-cell" EXACT [] synonym: "gamma-delta intraepithelial T-lymphocyte" EXACT [] synonym: "IEL" BROAD [] synonym: "intraepithelial lymphocyte" BROAD [] -xref: ZFA:0009339 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009339 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000800 {is_inferred="true"} ! mature gamma-delta T cell is_a: CL:0002496 ! intraepithelial lymphocyte intersection_of: CL:0000800 ! mature gamma-delta T cell @@ -9589,7 +9605,7 @@ synonym: "memory T lymphocyte" EXACT [] synonym: "memory T-cell" EXACT [] synonym: "memory T-lymphocyte" EXACT [] xref: BTO:0003435 -xref: ZFA:0009342 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009342 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002419 {is_inferred="true"} ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: bearer_of PATO:0001603 ! increased life span @@ -9662,7 +9678,7 @@ synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] synonym: "newly formed B cell" EXACT [ISBN:781735149] -xref: ZFA:0009343 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009343 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030044 GO:0045190 ! has_not_completed isotype switching @@ -9685,7 +9701,7 @@ subset: human_reference_atlas synonym: "pre-B cell" RELATED [] xref: BTO:0001133 xref: CALOHA:TS-0819 -xref: ZFA:0009344 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009344 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex @@ -9709,7 +9725,7 @@ synonym: "transitional B cell" EXACT [PMID:22343568] synonym: "transitional stage B lymphocyte" EXACT [] synonym: "transitional stage B-cell" EXACT [] synonym: "transitional stage B-lymphocyte" EXACT [] -xref: ZFA:0009345 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009345 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030044 GO:0002335 ! has_not_completed mature B cell differentiation @@ -9822,7 +9838,7 @@ comment: In mouse the NKR are Ly49 molecules and in human these cells express KI subset: cellxgene_subset synonym: "immature NK cell" EXACT [] synonym: "p-NK" RELATED [PMID:12457618] -xref: ZFA:0009346 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009346 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000623 ! natural killer cell is_a: CL:0001082 ! immature innate lymphoid cell intersection_of: CL:0000623 ! natural killer cell @@ -9839,7 +9855,7 @@ subset: human_reference_atlas synonym: "LAK cell" BROAD [PMID:14685782] synonym: "lymphokine activated killer cell" BROAD [PMID:14685782] synonym: "mature NK cell" EXACT [] -xref: ZFA:0009347 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009347 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000623 ! natural killer cell relationship: RO:0002202 CL:0000823 ! develops from immature natural killer cell property_value: RO:0002175 NCBITaxon:9606 @@ -9854,7 +9870,7 @@ synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] -xref: ZFA:0009348 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein @@ -9888,7 +9904,7 @@ synonym: "progenitor B lymphocyte" EXACT [] synonym: "progenitor B-cell" EXACT [] synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 -xref: ZFA:0009349 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 @@ -9910,7 +9926,7 @@ synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] synonym: "progenitor T cell" EXACT [] synonym: "TN1 cell" NARROW [] -xref: ZFA:0009350 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009350 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation @@ -9922,7 +9938,7 @@ id: CL:0000828 name: thromboblast def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. -xref: ZFA:0009351 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009351 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell @@ -10042,7 +10058,7 @@ name: neutrophil progenitor cell def: "A progenitor cell of the neutrophil lineage." [GOC:add, GOC:tfm, ISBN:0721601464] subset: cellxgene_subset synonym: "neutrophil stem cell" RELATED [] -xref: ZFA:0009352 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009352 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell intersection_of: CL:0002191 ! granulocytopoietic cell @@ -10056,7 +10072,7 @@ name: myeloblast def: "The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow." [GOC:add, http://en.wikipedia.org/wiki/Myeloblast, http://www.cap.org, ISBN:0721601464] xref: BTO:0000187 xref: FMA:83524 -xref: ZFA:0009353 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009353 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell intersection_of: CL:0002191 ! granulocytopoietic cell @@ -10114,7 +10130,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell @@ -10162,7 +10178,7 @@ synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 xref: FMA:70338 -xref: ZFA:0009355 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009355 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -10181,7 +10197,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -10239,7 +10255,7 @@ synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 xref: CALOHA:TS-0768 xref: FMA:86713 -xref: ZFA:0009357 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009357 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte @@ -10343,7 +10359,7 @@ name: ciliated olfactory receptor neuron def: "An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob." [PMID:16841163] synonym: "ciliated olfactory sensory neuron" EXACT [] synonym: "ciliated sensory neuron" EXACT [] -xref: ZFA:0009358 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009358 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000064 ! ciliated cell is_a: CL:0000207 ! olfactory receptor cell intersection_of: CL:0000207 ! olfactory receptor cell @@ -10355,7 +10371,7 @@ name: microvillous olfactory receptor neuron def: "An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli." [PMID:16841163] synonym: "microvillous olfactory sensory neuron" EXACT [] synonym: "microvillous sensory neuron" RELATED [] -xref: ZFA:0009359 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009359 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000207 ! olfactory receptor cell [Term] @@ -10365,7 +10381,7 @@ def: "An olfactory receptor cell with short cilia growing in an invagination bor synonym: "crypt cell" EXACT [] synonym: "crypt olfactory sensory neuron" EXACT [] synonym: "crypt sensory neuron" EXACT [] -xref: ZFA:0009360 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009360 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000207 ! olfactory receptor cell [Term] @@ -10376,10 +10392,10 @@ def: "A neuron that releases serotonin as a neurotransmitter." [SANBI:mhl] synonym: "5-HT neuron" EXACT [] synonym: "5-hydroxytryptamine neuron" EXACT [] synonym: "serotinergic neuron" RELATED [] -xref: FBbt:00005133 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005133 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MESH:D059326 xref: WBbt:0006837 -xref: ZFA:0009361 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009361 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -10390,7 +10406,7 @@ relationship: capable_of GO:0060096 ! serotonin secretion, neurotransmission id: CL:0000851 name: neuromast mantle cell def: "Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded." [ISBN:0125296509] -xref: ZFA:0009362 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009362 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell disjoint_from: CL:0000855 ! sensory hair cell relationship: part_of UBERON:0008904 ! neuromast @@ -10400,7 +10416,7 @@ id: CL:0000852 name: neuromast supporting cell def: "Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells." [ISBN:0125296509] synonym: "neuromast support cell" EXACT [] -xref: ZFA:0009363 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009363 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell disjoint_from: CL:0000855 ! sensory hair cell relationship: part_of UBERON:0008904 ! neuromast @@ -10414,7 +10430,7 @@ synonym: "olfactory sustentacular cell" EXACT [] synonym: "supporting cell of olfactory epithelium" EXACT [] synonym: "sustentaculocyte of olfactory epithelium" EXACT [] xref: FMA:62302 -xref: ZFA:0009364 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009364 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell is_a: CL:0002169 ! basal cell of olfactory epithelium intersection_of: CL:0000630 ! supporting cell @@ -10424,7 +10440,7 @@ intersection_of: part_of UBERON:0001997 ! olfactory epithelium id: CL:0000854 name: interneuromast cell def: "Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts." [SANBI:mhl] -xref: ZFA:0009365 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009365 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000133 ! neurectodermal cell relationship: RO:0002202 CL:0000032 ! develops from neuroplacodal cell @@ -10435,14 +10451,14 @@ name: sensory hair cell def: "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." [SANBI:mhl] synonym: "hair cell" BROAD [] xref: BTO:0004744 -xref: ZFA:0009366 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009366 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000199 ! mechanoreceptor cell [Term] id: CL:0000856 name: neuromast hair cell def: "Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface." [SANBI:mhl] -xref: ZFA:0009367 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009367 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000855 ! sensory hair cell @@ -10454,7 +10470,7 @@ relationship: part_of UBERON:0008904 ! neuromast id: CL:0000857 name: slow muscle myoblast def: "A skeletal muscle myoblast that differentiates into slow muscle fibers." [SANBI:mhl] -xref: ZFA:0009368 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009368 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000189 ! develops into slow muscle cell @@ -10464,7 +10480,7 @@ relationship: RO:0002203 CL:0000189 ! develops into slow muscle cell id: CL:0000858 name: fast muscle myoblast def: "A skeletal muscle myoblast that differentiates into fast muscle fibers." [SANBI:mhl] -xref: ZFA:0009369 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009369 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000190 ! develops into fast muscle cell @@ -11071,8 +11087,8 @@ intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: bearer_of PATO:0001603 ! increased life span intersection_of: output_of GO:0002286 ! T cell activation involved in immune response intersection_of: output_of GO:0043379 ! memory T cell differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0000898 @@ -11341,8 +11357,8 @@ intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: bearer_of PATO:0001603 ! increased life span intersection_of: output_of GO:0002286 ! T cell activation involved in immune response intersection_of: output_of GO:0043379 ! memory T cell differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0000910 @@ -12713,7 +12729,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -13431,7 +13447,7 @@ comment: It has been noted in at least some mammalian species that granule cells subset: cellxgene_subset synonym: "granule cell of the cerebellum" EXACT [doi:10.3389/fncir.2020.611841] xref: BTO:0004278 -xref: ZFA:0001691 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0001691 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000120 ! granule cell is_a: CL:2000028 ! cerebellum glutamatergic neuron is_a: UBERON:0004121 ! ectoderm-derived structure @@ -13464,7 +13480,7 @@ name: cell in vitro def: "A cell that is maintained or propagated in a controlled artificial environment for use in an investigation." [ReO:mhb] comment: 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-01-12T09:58:38Z [Term] @@ -13477,8 +13493,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 creation_date: 2011-11-16T04:28:16Z [Term] @@ -13865,7 +13881,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -13879,8 +13895,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0000460 ! abnormal relationship: bearer_of PATO:0000460 ! abnormal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T18:53:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T18:53:32Z" xsd:dateTime [Term] id: CL:0001062 @@ -13920,8 +13936,8 @@ is_a: CL:0001061 ! abnormal cell intersection_of: CL:0001061 ! abnormal cell intersection_of: bearer_of PATO:0002011 ! neoplastic relationship: bearer_of PATO:0002011 ! neoplastic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T19:16:26Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T19:16:26Z" xsd:dateTime [Term] id: CL:0001064 @@ -13935,8 +13951,8 @@ is_a: CL:0001063 ! neoplastic cell intersection_of: CL:0001063 ! neoplastic cell intersection_of: bearer_of PATO:0002097 ! neoplastic, malignant relationship: bearer_of PATO:0002097 ! neoplastic, malignant -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T19:39:12Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T19:39:12Z" xsd:dateTime [Term] id: CL:0001065 @@ -13955,9 +13971,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:20:48Z" xsd:dateTime [Term] id: CL:0001066 @@ -14009,17 +14025,17 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032609 ! type II interferon production -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:42:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:42:44Z" xsd:dateTime [Term] id: CL:0001068 name: ILC1 def: "A group 1 innate lymphoid cell that is non-cytotoxic." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417] is_a: CL:0001067 ! group 1 innate lymphoid cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:54:12Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:54:12Z" xsd:dateTime [Term] id: CL:0001069 @@ -14034,9 +14050,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032634 ! interleukin-5 production relationship: capable_of GO:0032634 ! interleukin-5 production -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T21:20:08Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T21:20:08Z" xsd:dateTime [Term] id: CL:0001070 @@ -14065,9 +14081,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-31T20:21:26Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-31T20:21:26Z" xsd:dateTime [Term] id: CL:0001072 @@ -14250,9 +14266,9 @@ relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002202 CL:0000905 ! develops from effector memory CD4-positive, alpha-beta T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2021-01-18T16:32:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2021-01-18T16:32:44Z" xsd:dateTime [Term] id: CL:0001200 @@ -14267,7 +14283,7 @@ intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001201 @@ -14284,7 +14300,7 @@ intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001202 @@ -14296,7 +14312,7 @@ is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: RO:0002104 PR:000001412 ! has plasma membrane part CD86 molecule relationship: RO:0002104 PR:000001412 ! has plasma membrane part CD86 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001203 @@ -14352,7 +14368,7 @@ relationship: RO:0015015 PR:000001381 ! has high plasma membrane amount interleu [Term] id: CL:0001658 name: visual pigment cell (sensu Nematoda and Protostomia) -xref: FBbt:00004230 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004230 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000149 ! visual pigment cell is_a: CL:0000341 ! pigment cell (sensu Nematoda and Protostomia) @@ -14381,7 +14397,7 @@ relationship: CL:4030046 PR:000009127 ! lacks_plasma_membrane_part integrin alph relationship: RO:0002104 PR:000001345 ! has plasma membrane part endoglin relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002202 CL:0002006 ! develops from Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:14:16Z [Term] @@ -14397,7 +14413,7 @@ intersection_of: RO:0002104 PR:000001865 ! has plasma membrane part interleukin- relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0002202 CL:0001026 ! develops from CD34-positive, CD38-positive common myeloid progenitor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:19:22Z [Term] @@ -14424,7 +14440,7 @@ relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell relationship: RO:0002202 CL:0001023 ! develops from Kit-positive, CD34-positive common myeloid progenitor relationship: RO:0015015 GO:0033001 ! has high plasma membrane amount Fc-gamma receptor III complex relationship: RO:0015015 PR:000001479 ! has high plasma membrane amount low affinity immunoglobulin gamma Fc region receptor II -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:19:28Z [Term] @@ -14440,7 +14456,7 @@ intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecul relationship: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002202 CL:0002005 ! develops from CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:14:30Z [Term] @@ -14455,7 +14471,7 @@ intersection_of: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophori relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A relationship: RO:0002202 CL:0002003 ! develops from CD34-positive, GlyA-negative erythroid progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:31:50Z [Term] @@ -14473,7 +14489,7 @@ relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:43:10Z [Term] @@ -14497,7 +14513,7 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0015016 GO:0033001 ! has low plasma membrane amount Fc-gamma receptor III complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:43:12Z [Term] @@ -14514,7 +14530,7 @@ intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/s relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002202 CL:0002002 ! develops from Kit-positive granulocyte monocyte progenitor relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-14T03:25:15Z [Term] @@ -14529,7 +14545,7 @@ intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl intersection_of: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002202 CL:0002001 ! develops from CD34-positive, CD38-positive granulocyte monocyte progenitor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-14T03:25:17Z [Term] @@ -14547,7 +14563,7 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -14610,7 +14626,7 @@ relationship: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type t relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: RO:0002202 CL:0002002 ! develops from Kit-positive granulocyte monocyte progenitor relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-26T02:43:40Z [Term] @@ -14631,7 +14647,7 @@ relationship: RO:0002104 PR:000002981 ! has plasma membrane part lymphocyte anti relationship: RO:0002202 CL:0002000 ! develops from Kit-positive erythroid progenitor cell relationship: RO:0015015 PR:000001945 ! has high plasma membrane amount transferrin receptor protein 1 relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:31:56Z [Term] @@ -14646,7 +14662,7 @@ intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin- relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002202 CL:0002004 ! develops from CD34-negative, GlyA-negative proerythroblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:41:15Z [Term] @@ -14665,7 +14681,7 @@ relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cel relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002202 CL:0002012 ! develops from Kit-low proerythroblast relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:41:22Z [Term] @@ -14684,7 +14700,7 @@ relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cel relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002202 CL:0002014 ! develops from Kit-negative, Ly-76 high basophilic erythroblast relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:53:11Z [Term] @@ -14699,7 +14715,7 @@ intersection_of: RO:0015016 PR:000001945 ! has low plasma membrane amount transf relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002202 CL:0002013 ! develops from GlyA-positive basophilic erythroblast relationship: RO:0015016 PR:000001945 ! has low plasma membrane amount transferrin receptor protein 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:53:16Z [Term] @@ -14720,7 +14736,7 @@ relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte an relationship: RO:0002202 CL:0002015 ! develops from Kit-negative, Ly-76 high polychromatophilic erythroblast relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) relationship: RO:0015016 PR:000001945 ! has low plasma membrane amount transferrin receptor protein 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:04:15Z [Term] @@ -14735,7 +14751,7 @@ intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin- relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002202 CL:0002016 ! develops from CD71-low, GlyA-positive polychromatic erythroblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:04:21Z [Term] @@ -14748,7 +14764,7 @@ intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) relationship: RO:0002202 CL:0002017 ! develops from Kit-negative, Ly-76 high orthochromatophilic erythroblasts relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:37:00Z [Term] @@ -14761,7 +14777,7 @@ intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002202 CL:0002018 ! develops from CD71-negative, GlyA-positive orthochromatic erythroblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:48:25Z [Term] @@ -14774,7 +14790,7 @@ intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002202 CL:0002020 ! develops from GlyA-positive reticulocytes -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:51:22Z [Term] @@ -14787,7 +14803,7 @@ intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) relationship: RO:0002202 CL:0002019 ! develops from Ly-76 high reticulocyte relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:51:27Z [Term] @@ -14804,7 +14820,7 @@ relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002202 CL:0002025 ! develops from CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T02:39:09Z [Term] @@ -14829,7 +14845,7 @@ relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule relationship: RO:0002202 CL:0002006 ! develops from Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell relationship: RO:0015016 PR:000001479 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0015016 PR:000001483 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor III -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T02:39:15Z [Term] @@ -14846,7 +14862,7 @@ relationship: CL:4030046 PR:000001907 ! lacks_plasma_membrane_part platelet glyc relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002202 CL:0002005 ! develops from CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T03:52:47Z [Term] @@ -14863,7 +14879,7 @@ relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002202 CL:0002023 ! develops from CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T03:59:22Z [Term] @@ -14878,7 +14894,7 @@ intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alp relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002202 CL:0002024 ! develops from Kit-positive megakaryocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T10:39:07Z [Term] @@ -14908,7 +14924,7 @@ relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T12:46:33Z [Term] @@ -14926,7 +14942,7 @@ relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type t relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000009143 ! has plasma membrane part integrin beta-7 relationship: RO:0002202 CL:0002044 ! develops from Kit-positive, integrin beta7-high basophil mast progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T01:22:19Z [Term] @@ -14943,7 +14959,7 @@ intersection_of: RO:0015015 PR:000007431 ! has high plasma membrane amount high relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002202 CL:0002044 ! develops from Kit-positive, integrin beta7-high basophil mast progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T01:22:32Z [Term] @@ -14958,7 +14974,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -14973,7 +14989,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -14991,7 +15007,7 @@ intersection_of: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family relationship: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-type tyrosine-protein kinase FLT3 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002202 CL:0002034 ! develops from long term hematopoietic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T09:19:25Z [Term] @@ -15010,7 +15026,7 @@ intersection_of: RO:0015016 PR:000001843 ! has low plasma membrane amount Thy-1 relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-type tyrosine-protein kinase FLT3 relationship: RO:0015016 PR:000001843 ! has low plasma membrane amount Thy-1 membrane glycoprotein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T09:19:28Z [Term] @@ -15029,7 +15045,7 @@ relationship: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-type relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002202 CL:0002036 ! develops from Slamf1-positive multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T11:16:33Z [Term] @@ -15048,7 +15064,7 @@ relationship: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family mem relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 relationship: RO:0002202 CL:0002033 ! develops from short term hematopoietic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T11:16:35Z [Term] @@ -15064,7 +15080,7 @@ intersection_of: RO:0002104 PR:000001839 ! has plasma membrane part T-cell surfa relationship: RO:0002104 PR:000001083 ! has plasma membrane part CD2 molecule relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001839 ! has plasma membrane part T-cell surface glycoprotein CD5 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-20T02:20:43Z [Term] @@ -15097,8 +15113,8 @@ relationship: has_part PR:000003450 ! B-cell lymphoma 6 protein relationship: RO:0002104 PR:000001209 ! has plasma membrane part C-X-C chemokine receptor type 5 relationship: RO:0002104 PR:000001860 ! has plasma membrane part inducible T-cell costimulator relationship: RO:0002104 PR:000001919 ! has plasma membrane part programmed cell death protein 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:01:27Z [Term] @@ -15117,7 +15133,7 @@ relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like pr relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: RO:0015016 PR:000001004 ! has low plasma membrane amount CD4 molecule relationship: RO:0015016 PR:000025402 ! has low plasma membrane amount T cell receptor co-receptor CD8 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:09:16Z [Term] @@ -15135,7 +15151,7 @@ relationship: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: RO:0002202 CL:0002039 ! develops from immature NK T cell stage I relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:13:43Z [Term] @@ -15154,7 +15170,7 @@ relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002202 CL:0002040 ! develops from immature NK T cell stage II relationship: RO:0015016 PR:000001008 ! has low plasma membrane amount integrin alpha-2 relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:14:48Z [Term] @@ -15174,8 +15190,8 @@ relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002202 CL:0002041 ! develops from immature NK T cell stage III relationship: RO:0015015 PR:000001008 ! has high plasma membrane amount integrin alpha-2 relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:17:38Z [Term] @@ -15193,7 +15209,7 @@ relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: CL:4030046 PR:000001843 ! lacks_plasma_membrane_part Thy-1 membrane glycoprotein relationship: RO:0002202 CL:0001024 ! develops from CD34-positive, CD38-negative hematopoietic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-12T11:14:15Z [Term] @@ -15213,7 +15229,7 @@ relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte an relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III relationship: RO:0015015 PR:000009143 ! has high plasma membrane amount integrin beta-7 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T01:22:38Z [Term] @@ -15240,7 +15256,7 @@ relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T10:50:07Z [Term] @@ -15269,7 +15285,7 @@ relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015016 PR:000001898 ! has low plasma membrane amount neprilysin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T11:19:11Z [Term] @@ -15287,7 +15303,7 @@ intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal trans relationship: CL:4030046 PR:000002039 ! lacks_plasma_membrane_part glutamyl aminopeptidase relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002202 CL:0002045 ! develops from fraction A pre-pro B cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T11:56:21Z [Term] @@ -15307,7 +15323,7 @@ relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0002202 CL:0002046 ! develops from early pro-B cell relationship: RO:0015016 PR:000001002 ! has low plasma membrane amount CD19 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T12:06:06Z [Term] @@ -15333,7 +15349,7 @@ relationship: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminop relationship: RO:0002104 PR:000003457 ! has plasma membrane part V(D)J recombination-activating protein 1 relationship: RO:0002104 PR:000003460 ! has plasma membrane part V(D)J recombination-activating protein 2 relationship: RO:0002202 CL:0002047 ! develops from fraction B precursor B cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:04:01Z [Term] @@ -15357,7 +15373,7 @@ relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminopeptidase relationship: RO:0002202 CL:0002049 ! develops from fraction C precursor B cell relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:13:46Z [Term] @@ -15373,7 +15389,7 @@ intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-r relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 relationship: RO:0002202 CL:0002048 ! develops from late pro-B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:27:47Z [Term] @@ -15401,7 +15417,7 @@ relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 r relationship: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminopeptidase relationship: RO:0002202 CL:0002050 ! develops from fraction C' precursor B cell relationship: RO:0015016 PR:000001879 ! has low plasma membrane amount leukosialin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:55:16Z [Term] @@ -15417,7 +15433,7 @@ intersection_of: RO:0015016 PR:000001408 ! has low plasma membrane amount ADP-ri relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 relationship: RO:0002202 CL:0002051 ! develops from CD38-high pre-BCR positive cell relationship: RO:0015016 PR:000001408 ! has low plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T03:04:48Z [Term] @@ -15439,7 +15455,7 @@ relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transduc relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor relationship: RO:0002202 CL:0002052 ! develops from fraction D precursor B cell relationship: RO:0015016 PR:000001879 ! has low plasma membrane amount leukosialin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T03:13:47Z [Term] @@ -15458,7 +15474,7 @@ relationship: RO:0002202 CL:0002053 ! develops from CD22-positive, CD38-low smal relationship: RO:0015015 PR:000001288 ! has high plasma membrane amount B-cell receptor CD22 relationship: RO:0015016 PR:000001338 ! has low plasma membrane amount complement receptor type 2 relationship: RO:0015016 PR:000001898 ! has low plasma membrane amount neprilysin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T03:19:14Z [Term] @@ -15482,7 +15498,7 @@ relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobuli relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 relationship: RO:0002202 CL:0002054 ! develops from fraction E immature B cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-30T03:01:48Z [Term] @@ -15503,7 +15519,7 @@ intersection_of: RO:0002104 PR:000001925 ! has plasma membrane part scavenger re relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III relationship: RO:0002104 PR:000001465 ! has plasma membrane part high affinity immunoglobulin gamma Fc receptor I relationship: RO:0002104 PR:000001925 ! has plasma membrane part scavenger receptor cysteine-rich type 1 protein M130 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-05T08:25:41Z [Term] @@ -15526,7 +15542,7 @@ relationship: RO:0002104 PR:000001206 ! has plasma membrane part CX3C chemokine relationship: RO:0002202 CL:0002398 ! develops from Gr1-positive, CD43-positive monocyte relationship: RO:0015016 PR:000001199 ! has low plasma membrane amount C-C chemokine receptor type 2 relationship: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-05T08:25:44Z [Term] @@ -15540,8 +15556,8 @@ is_a: CL:0000941 {is_inferred="true"} ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-07T02:48:36Z [Term] @@ -15550,7 +15566,7 @@ name: melanophage def: "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes." [GOC:tfm, PMID:20479296, PMID:2943821] is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage relationship: part_of UBERON:0002097 ! skin of body -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-22T10:46:12Z [Term] @@ -15568,17 +15584,17 @@ intersection_of: RO:0002104 PR:000008982 ! has plasma membrane part interleukin- relationship: capable_of GO:0002215 ! defense response to nematode relationship: capable_of GO:0032638 ! interleukin-9 production relationship: RO:0002104 PR:000008982 ! has plasma membrane part interleukin-17 receptor B -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-22T11:18:44Z [Term] id: CL:0002062 -name: type I pneumocyte -def: "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." [GOC:tfm, http://www.copewithcytokines.de, PMID:20054144] +name: pulmonary alveolar type 1 cell +def: "A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." [GOC:tfm, http://www.copewithcytokines.de, PMID:20054144, PMID:29463737] subset: cellxgene_subset subset: human_reference_atlas -synonym: "AT1" EXACT [] -synonym: "ATI" EXACT [] +synonym: "AT1" RELATED OMO:0003000 [PMID:29463737] +synonym: "ATI" RELATED OMO:0003000 [] synonym: "lung type 1 cells" EXACT [] synonym: "membranous pneumocytes" EXACT [] synonym: "pulmonary alveolar type I cell" EXACT [] @@ -15586,51 +15602,52 @@ synonym: "small alveolar cells" EXACT [] synonym: "squamous alveolar cell" EXACT [] synonym: "squamous alveolar lining cell" EXACT [] synonym: "type 1 alveolar epithelial cells" EXACT [] -synonym: "type 1 pneumocyte" EXACT [] +synonym: "type 1 pneumocyte" EXACT [PMID:32491474] synonym: "type I alveolar cells" EXACT [] synonym: "type I alveolar epithelial cells" EXACT [] +synonym: "type I pneumocyte" EXACT [] xref: BTO:0000780 xref: FMA:62500 -is_a: CL:0000322 ! pneumocyte -intersection_of: CL:0000322 ! pneumocyte +is_a: CL:0000322 ! pulmonary alveolar epithelial cell +intersection_of: CL:0000322 ! pulmonary alveolar epithelial cell intersection_of: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-23T04:37:54Z [Term] id: CL:0002063 -name: type II pneumocyte -def: "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli." [GOC:tfm, http://www.copewithcytokines.de, ISBN:0412046911, PMID:8540632] +name: pulmonary alveolar type 2 cell +def: "A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli." [GOC:tfm, http://www.copewithcytokines.de, ISBN:0412046911, PMID:36138472, PMID:8540632] subset: cellxgene_subset subset: human_reference_atlas -synonym: "AT2" EXACT [] -synonym: "ATII" EXACT [] +synonym: "AT2" RELATED OMO:0003000 [PMID:36138472] +synonym: "ATII" RELATED OMO:0003000 [] synonym: "cuboidal type II cell" EXACT [] synonym: "granular pneumocyte" EXACT [] synonym: "great alveolar cell" EXACT [] synonym: "lung type 2 cell" EXACT [] synonym: "lung type II cell" RELATED [] -synonym: "TII" EXACT [] +synonym: "TII" RELATED [] synonym: "type 2 alveolar epithelial cell" EXACT [] synonym: "type 2 alveolocyte" EXACT [] synonym: "type 2 pneumocyte" EXACT [] synonym: "type II alveolar cell" EXACT [] synonym: "type II alveolar epithelial cell" EXACT [] synonym: "type II alveolocyte" EXACT [] +synonym: "type II pneumocyte" EXACT [PMID:32491474] xref: BTO:0000538 xref: FMA:62501 -is_a: BFO:0000002 is_a: CL:0000157 ! surfactant secreting cell -is_a: CL:0000322 ! pneumocyte +is_a: CL:0000322 ! pulmonary alveolar epithelial cell is_a: CL:1000272 ! lung secretory cell -intersection_of: CL:0000322 ! pneumocyte +intersection_of: CL:0000322 ! pulmonary alveolar epithelial cell intersection_of: capable_of GO:0032940 ! secretion by cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis -relationship: RO:0002202 CL:4040003 ! develops from fetal pre-type II pneumocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +relationship: RO:0002202 CL:4040003 ! develops from fetal pre-type II pulmonary alveolar epithelial cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-24T12:04:13Z [Term] @@ -15643,15 +15660,15 @@ synonym: "acinar cell of pancreas" EXACT [] xref: BTO:0000028 xref: CALOHA:TS-0737 xref: FMA:63032 -xref: ZFA:0005739 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005739 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000622 {is_inferred="true"} ! acinar cell is_a: CL:1001599 ! pancreas exocrine glandular cell intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0001263 ! pancreatic acinus relationship: has_part GO:0042589 ! zymogen granule membrane relationship: part_of UBERON:0001263 ! pancreatic acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-24T03:16:29Z [Term] @@ -15664,7 +15681,7 @@ synonym: "P cell" RELATED OMO:0003000 [] synonym: "respiratory enterochromaffin cell" EXACT [] xref: FMA:14118 is_a: CL:0000165 ! neuroendocrine cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-28T08:24:30Z [Term] @@ -15676,7 +15693,7 @@ is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000170 ! glucagon secreting cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: capable_of GO:0070091 ! glucagon secretion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T10:48:54Z [Term] @@ -15690,8 +15707,8 @@ synonym: "Purkinje muscle cell" EXACT [] xref: BTO:0001032 xref: FMA:14146 is_a: CL:0002086 ! specialized cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-28T08:36:15Z [Term] @@ -15703,7 +15720,7 @@ synonym: "type 2 vestibular sensory cell" EXACT [] synonym: "type II hair cell" EXACT [] xref: FMA:67909 is_a: CL:0000609 ! vestibular hair cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T09:58:13Z [Term] @@ -15715,7 +15732,7 @@ synonym: "type 1 vestibular sensory cell" EXACT [] synonym: "type I hair cell" EXACT [] xref: FMA:62352 is_a: CL:0000609 ! vestibular hair cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T09:58:19Z [Term] @@ -15735,8 +15752,8 @@ is_a: CL:0002253 {is_inferred="true"} ! epithelial cell of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001278 ! epithelium of large intestine relationship: part_of UBERON:0001278 ! epithelium of large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T11:07:25Z [Term] @@ -15750,7 +15767,7 @@ synonym: "pacemaker cell" BROAD [] xref: BTO:0004190 xref: FMA:67101 is_a: CL:0002086 ! specialized cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T11:41:37Z [Term] @@ -15759,7 +15776,7 @@ name: transitional myocyte def: "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." [FMA:67142, GOC:tfm] xref: FMA:67142 is_a: CL:0002086 ! specialized cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T02:39:32Z [Term] @@ -15769,7 +15786,7 @@ def: "The myoendocrine cellis a specialized myocyte localized mainly in the righ xref: FMA:67111 is_a: CL:0000163 ! endocrine cell is_a: CL:0002086 ! specialized cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T11:50:47Z [Term] @@ -15781,8 +15798,8 @@ synonym: "pulmonary brush cell" RELATED [] is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002204 ! brush cell intersection_of: CL:0002204 ! brush cell -intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: part_of UBERON:0008397 ! tracheobronchial epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:22:46Z [Term] @@ -15790,11 +15807,13 @@ id: CL:0002076 name: endo-epithelial cell def: "An epithelial cell derived from endoderm." [FMA:69075, GOC:tfm] xref: FMA:69075 -xref: ZFA:0009383 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009383 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: RO:0002202 CL:0000223 ! develops from endodermal cell relationship: RO:0002202 CL:0000223 ! develops from endodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:14Z [Term] @@ -15802,13 +15821,13 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -15817,13 +15836,13 @@ name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -15833,7 +15852,7 @@ def: "Epithelial cell found in the ducts of the pancreas. This cell type contrib subset: cellxgene_subset subset: human_reference_atlas xref: FMA:63099 -xref: ZFA:0009380 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009380 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:1001433 ! epithelial cell of exocrine pancreas intersection_of: CL:0000083 ! epithelial cell of pancreas @@ -15841,8 +15860,8 @@ intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter a intersection_of: part_of UBERON:0001064 ! ventral pancreatic duct relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity relationship: part_of UBERON:0001064 ! ventral pancreatic duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-30T08:49:43Z [Term] @@ -15853,15 +15872,15 @@ subset: human_reference_atlas synonym: "centroacinar cell of Langerhans" EXACT [] synonym: "pancreatic centroacinar cell" EXACT [] xref: FMA:62455 -xref: ZFA:0005740 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005740 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1001433 ! epithelial cell of exocrine pancreas intersection_of: CL:0000083 ! epithelial cell of pancreas intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0001263 ! pancreatic acinus relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity relationship: part_of UBERON:0001263 ! pancreatic acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-30T08:49:52Z [Term] @@ -15872,15 +15891,15 @@ synonym: "sheath cell of carotid body" EXACT [] xref: FMA:84187 is_a: CL:0000703 ! sustentacular cell is_a: CL:0002256 ! supporting cell of carotid body -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-30T04:23:42Z [Term] id: CL:0002082 name: type II cell of adrenal medulla def: "A chromaffin cell of the adrenal medulla that produces epinephrine." [GOC:tfm] -synonym: "adremergic chromaffin cell" EXACT [] synonym: "adrenal secreting cell of the adrenal medulla" EXACT [] +synonym: "adrenergic chromaffin cell" EXACT [] synonym: "epiniphrine secreting cell of the adrenal medulla" EXACT [] xref: FMA:69322 is_a: CL:0000336 {is_inferred="true"} ! adrenal medulla chromaffin cell @@ -15888,7 +15907,7 @@ is_a: CL:0000454 ! epinephrine secreting cell intersection_of: CL:0000336 ! adrenal medulla chromaffin cell intersection_of: capable_of GO:0048242 ! epinephrine secretion intersection_of: part_of UBERON:0001236 ! adrenal medulla -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-14T09:41:42Z [Term] @@ -15902,7 +15921,7 @@ is_a: CL:0000459 ! noradrenergic cell intersection_of: CL:0000336 ! adrenal medulla chromaffin cell intersection_of: capable_of GO:0048243 ! norepinephrine secretion intersection_of: part_of UBERON:0001236 ! adrenal medulla -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-14T10:12:24Z [Term] @@ -15913,7 +15932,7 @@ synonym: "Boettcher's cell" EXACT [] synonym: "Bottcher cell" EXACT [] synonym: "Bottcher's cell" EXACT [] is_a: CL:0002315 ! supporting cell of cochlea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-14T03:22:02Z [Term] @@ -15926,7 +15945,7 @@ synonym: "stretch cell" EXACT [] xref: BTO:0001953 xref: FMA:54560 is_a: CL:0000683 ! ependymoglial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-15T11:21:11Z [Term] @@ -15935,7 +15954,7 @@ name: specialized cardiac myocyte def: "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." [FMA:67968, GOC:tfm] xref: FMA:67968 is_a: CL:0000746 ! cardiac muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-21T01:33:38Z [Term] @@ -15949,7 +15968,7 @@ is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: CL:4030045 GO:0030141 ! lacks_part secretory granule relationship: CL:4030045 GO:0030141 ! lacks_part secretory granule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T11:30:33Z [Term] @@ -15967,8 +15986,8 @@ is_a: CL:0000710 {is_inferred="true"} ! neurecto-epithelial cell intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: capable_of GO:0043134 ! regulation of hindgut contraction relationship: capable_of GO:0043134 ! regulation of hindgut contraction -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T03:26:00Z [Term] @@ -16012,7 +16031,7 @@ relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 r relationship: RO:0002104 PR:000008982 ! has plasma membrane part interleukin-17 receptor B relationship: RO:0002104 PR:000008994 ! has plasma membrane part interleukin-1 receptor-like 1 relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-12T02:22:19Z [Term] @@ -16025,7 +16044,7 @@ xref: MESH:D059705 xref: WBbt:0008429 xref: XAO:0000262 is_a: CL:0000021 ! female germ cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T09:49:53Z [Term] @@ -16039,7 +16058,7 @@ xref: EMAPA:16032 xref: FMA:18650 xref: VHOG:0000464 is_a: CL:0002090 ! polar body -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T09:49:58Z [Term] @@ -16055,7 +16074,7 @@ is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -16069,7 +16088,7 @@ xref: EMAPA:16034 xref: EMAPA:16045 xref: FMA:18651 is_a: CL:0002090 ! polar body -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T09:50:01Z [Term] @@ -16079,7 +16098,7 @@ def: "A cell that makes up the loose connective tissue of the ovary." [GOC:tfm] subset: cellxgene_subset xref: FMA:18709 is_a: CL:0002132 ! stromal cell of ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:11:34Z [Term] @@ -16091,8 +16110,8 @@ synonym: "hilar cell of ovary" EXACT [] xref: FMA:18710 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:18:18Z [Term] @@ -16105,7 +16124,7 @@ is_a: CL:0008009 ! transversely striated visceral muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0009966 ! internodal tract relationship: part_of UBERON:0009966 ! internodal tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:24:11Z [Term] @@ -16121,7 +16140,7 @@ is_a: CL:0002078 {is_inferred="true"} ! meso-epithelial cell is_a: CL:1001601 ! adrenal gland glandular cell intersection_of: CL:0002078 ! meso-epithelial cell intersection_of: part_of UBERON:0001235 ! adrenal cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:37:44Z [Term] @@ -16132,7 +16151,7 @@ synonym: "regular cardiac muscle cell" EXACT [] synonym: "regular cardiac muscle fiber" EXACT [] xref: FMA:67967 is_a: CL:0000746 ! cardiac muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:33:10Z [Term] @@ -16147,7 +16166,7 @@ is_a: CL:0002097 {is_inferred="true"} ! cortical cell of adrenal gland intersection_of: CL:0002097 ! cortical cell of adrenal gland intersection_of: part_of UBERON:0002053 ! zona glomerulosa of adrenal gland relationship: part_of UBERON:0002053 ! zona glomerulosa of adrenal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:42:02Z [Term] @@ -16156,7 +16175,7 @@ name: regular interventricular cardiac myocyte def: "A regular cardiac myocyte of the interventricular region of the heart." [GOC:tfm] xref: FMA:228792 is_a: CL:0002098 ! regular cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:40:52Z [Term] @@ -16467,7 +16486,7 @@ relationship: capable_of GO:0032609 ! type II interferon production relationship: output_of GO:0030217 ! T cell differentiation relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule relationship: RO:0002202 CL:0002126 ! develops from CD25-positive, CD27-positive immature gamma-delta T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-18T09:57:19Z [Term] @@ -16486,7 +16505,7 @@ relationship: CL:4030046 PR:000001963 ! lacks_plasma_membrane_part CD27 molecule relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: output_of GO:0030217 ! T cell differentiation relationship: RO:0002202 CL:0002126 ! develops from CD25-positive, CD27-positive immature gamma-delta T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-18T09:57:29Z [Term] @@ -16511,7 +16530,7 @@ relationship: RO:0015015 PR:000001318 ! has high plasma membrane amount L-select relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: RO:0015016 PR:000001083 ! has low plasma membrane amount CD2 molecule relationship: RO:0015016 PR:000001839 ! has low plasma membrane amount T-cell surface glycoprotein CD5 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-18T10:35:37Z [Term] @@ -16522,7 +16541,7 @@ is_a: CL:0000911 {is_inferred="true"} ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0045087 ! innate immune response relationship: capable_of GO:0045087 ! innate immune response -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-20T02:14:25Z [Term] @@ -16560,7 +16579,7 @@ synonym: "regular atrial cardiac muscle fiber" EXACT [] synonym: "regular cardiac muscle cell of atrium" EXACT [] xref: FMA:83108 is_a: CL:0002098 ! regular cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:41:03Z [Term] @@ -16569,7 +16588,7 @@ name: regular interatrial cardiac myocyte def: "A cardiac myocyte of the interatrial region of the heart." [GOC:tfm] xref: FMA:228790 is_a: CL:0002098 ! regular cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:41:09Z [Term] @@ -16583,7 +16602,7 @@ synonym: "ventricular cardiac muscle cell" BROAD [GOC:pr] synonym: "ventricular myocyte" EXACT [] xref: FMA:83109 is_a: CL:0002098 ! regular cardiac myocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:41:13Z [Term] @@ -16597,7 +16616,7 @@ is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T12:10:31Z [Term] @@ -16606,7 +16625,7 @@ name: stromal cell of ovarian cortex def: "A stromal cell of the ovarian cortex." [GOC:tfm] xref: FMA:256169 is_a: CL:0002132 ! stromal cell of ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T12:12:15Z [Term] @@ -16618,7 +16637,7 @@ is_a: CL:0002132 {is_inferred="true"} ! stromal cell of ovary intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0013192 ! ovarian medulla relationship: part_of UBERON:0013192 ! ovarian medulla -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T12:12:17Z [Term] @@ -16628,7 +16647,7 @@ def: "Epidermal cells that do not contain keratin. Cell type is usually associat xref: FMA:62880 is_a: CL:0000362 ! epidermal cell relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T08:43:27Z [Term] @@ -16639,7 +16658,7 @@ synonym: "type II cortical cell of adrenal gland" EXACT [] xref: FMA:69547 is_a: CL:0000460 ! glucocorticoid secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:50:42Z [Term] @@ -16649,7 +16668,7 @@ def: "A cell in the zona reticularis that produce sex hormones." [GOC:tfm, ISBN: xref: FMA:69564 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:50:44Z [Term] @@ -16664,13 +16683,12 @@ synonym: "lymphatic endothelial cell" EXACT [] xref: BTO:0004167 xref: FMA:68458 is_a: CL:0002139 {is_inferred="true"} ! endothelial cell of vascular tree -intersection_of: CL:0002139 ! endothelial cell of vascular tree +intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001473 ! lymphatic vessel -intersection_of: RO:0002202 CL:0005022 ! develops from vascular lymphangioblast relationship: part_of UBERON:0001473 ! lymphatic vessel relationship: RO:0002202 CL:0005022 ! develops from vascular lymphangioblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:05:28Z [Term] @@ -16685,7 +16703,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -16702,7 +16720,7 @@ is_a: CL:1000448 ! epithelial cell of sweat gland intersection_of: CL:0000317 ! sebum secreting cell intersection_of: part_of UBERON:0003487 ! skin sebaceous gland relationship: part_of UBERON:0003487 ! skin sebaceous gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T09:27:52Z [Term] @@ -16711,7 +16729,7 @@ name: active chief cell of parathyroid gland def: "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1" [FMA:0517223651, GOC:tfm] xref: FMA:69082 is_a: CL:0000446 ! chief cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T09:30:15Z [Term] @@ -16724,7 +16742,7 @@ is_a: CL:0000318 ! sweat secreting cell is_a: CL:0000434 ! eccrine cell is_a: CL:1000448 ! epithelial cell of sweat gland relationship: part_of UBERON:0000423 ! eccrine sweat gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:15:16Z [Term] @@ -16733,7 +16751,7 @@ name: dark chief cell of parathyroid gland def: "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." [GOC:tfm, ISBN:0721662544] xref: FMA:69080 is_a: CL:0000446 ! chief cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:18:36Z [Term] @@ -16745,12 +16763,13 @@ subset: human_reference_atlas xref: BTO:0004956 xref: CALOHA:TS-0112 xref: FMA:67756 +is_a: CL:0002653 ! squamous endothelial cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001915 ! endothelium of capillary relationship: part_of UBERON:0001915 ! endothelium of capillary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:15:00Z [Term] @@ -16764,8 +16783,8 @@ is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0005012 ! multi-ciliated epithelial cell is_a: CL:4030034 ! respiratory ciliated cell relationship: RO:0002202 CL:0002209 ! develops from intermediate epitheliocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:38:29Z [Term] @@ -16778,7 +16797,7 @@ is_a: CL:0000318 ! sweat secreting cell is_a: CL:0000434 ! eccrine cell is_a: CL:1000448 ! epithelial cell of sweat gland relationship: part_of UBERON:0000423 ! eccrine sweat gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:33:02Z [Term] @@ -16788,7 +16807,7 @@ def: "A chief cell of parathyroid glands that does not stain with hematoxylin or synonym: "clear chief cell of parathyroid cell" EXACT [] xref: FMA:69081 is_a: CL:0000446 ! chief cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:39:42Z [Term] @@ -16802,7 +16821,7 @@ is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002159 ! general ecto-epithelial cell intersection_of: part_of UBERON:0001754 ! dental pulp relationship: part_of UBERON:0001754 ! dental pulp -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:52:09Z [Term] @@ -16816,7 +16835,7 @@ is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:45:54Z [Term] @@ -16829,7 +16848,7 @@ synonym: "epitheloid macrophage" EXACT [] xref: FMA:83514 is_a: CL:0000235 ! macrophage relationship: RO:0002202 CL:0000861 ! develops from elicited macrophage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:48:30Z [Term] @@ -16839,7 +16858,7 @@ def: "A promyelocyte that is considerably smaller, with more condensed chromatin subset: cellxgene_subset xref: FMA:83534 is_a: CL:0000836 ! promyelocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:07:50Z [Term] @@ -16849,7 +16868,7 @@ def: "A columnar cell of the cervix uteri." [GOC:tfm, ISBN:0721662544] xref: FMA:86486 is_a: CL:0002149 ! epithelial cell of uterus relationship: part_of UBERON:0000458 ! endocervix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:47:47Z [Term] @@ -16864,8 +16883,8 @@ is_a: CL:0000225 ! anucleate cell is_a: CL:0000311 ! keratin accumulating cell relationship: part_of UBERON:0002027 ! stratum corneum of epidermis relationship: RO:0002202 CL:0000312 ! develops from keratinocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:53:03Z [Term] @@ -16875,7 +16894,7 @@ def: "A promyelocyte with a nucleus that is indented and contains more marginate subset: cellxgene_subset xref: FMA:83533 is_a: CL:0000836 ! promyelocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:07:53Z [Term] @@ -16885,7 +16904,7 @@ def: "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the re synonym: "burr cell" EXACT [] xref: FMA:81099 is_a: CL:0000595 ! enucleate erythrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:15:21Z [Term] @@ -16897,7 +16916,7 @@ xref: FMA:86495 is_a: CL:0001035 ! bone cell is_a: CL:0002078 ! meso-epithelial cell relationship: part_of UBERON:0009859 ! endosteum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:33:58Z [Term] @@ -16906,7 +16925,7 @@ name: external epithelial cell of tympanic membrane def: "Epithelial cell found on the external side of the tympanic membrane" [GOC:tfm, PMID:5686391] xref: FMA:70558 is_a: CL:0002159 ! general ecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:25:31Z [Term] @@ -16915,7 +16934,7 @@ name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:31:08Z [Term] @@ -16923,7 +16942,7 @@ id: CL:0002160 name: basal external epithelial cell of tympanic membrane def: "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions." [PMID:5686391] is_a: CL:0002158 ! external epithelial cell of tympanic membrane -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:28:44Z [Term] @@ -16931,7 +16950,7 @@ id: CL:0002161 name: superficial external epithelial cell of tympanic membrane def: "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus." [PMID:5686391] is_a: CL:0002158 ! external epithelial cell of tympanic membrane -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:28:48Z [Term] @@ -16941,7 +16960,7 @@ def: "An extremely flattened cell type found on the inner side of the tympanic m xref: FMA:70626 is_a: CL:0002076 ! endo-epithelial cell relationship: part_of UBERON:0002364 ! tympanic membrane -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:49:46Z [Term] @@ -16950,7 +16969,7 @@ name: internal pillar cell of cochlea def: "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] xref: FMA:75726 is_a: CL:1000191 ! pillar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T11:05:21Z [Term] @@ -16959,7 +16978,7 @@ name: external pillar cell of cochlea def: "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] xref: FMA:75727 is_a: CL:1000191 ! pillar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T11:05:23Z [Term] @@ -16968,7 +16987,7 @@ name: phalangeal cell def: "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." [GOC:tfm, ISBN:0618947256] xref: FMA:79800 is_a: CL:0002490 ! organ of Corti supporting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T01:29:07Z [Term] @@ -16981,7 +17000,7 @@ xref: FMA:62987 is_a: CL:0002159 {is_inferred="true"} ! general ecto-epithelial cell is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0011595 ! jaw region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:51:27Z [Term] @@ -16995,7 +17014,7 @@ is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell relationship: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:47:13Z [Term] @@ -17004,7 +17023,7 @@ name: border cell of cochlea def: "A border cell is a slender columnar cell on the medial portion of the basilar membrane." [FMA:0412046911, GOC:tfm] xref: FMA:79798 is_a: CL:0002315 ! supporting cell of cochlea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T01:47:12Z [Term] @@ -17016,10 +17035,11 @@ synonym: "horizontal basal cell" BROAD [] xref: FMA:62303 is_a: CL:0002167 {is_inferred="true"} ! olfactory epithelial cell is_a: CL:0002319 ! neural cell +is_a: CL:0002631 ! epithelial cell of upper respiratory tract intersection_of: CL:0002167 ! olfactory epithelial cell intersection_of: part_of UBERON:0001997 ! olfactory epithelium relationship: part_of UBERON:0001997 ! olfactory epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:58:54Z [Term] @@ -17032,7 +17052,7 @@ is_a: CL:0002336 ! buccal mucosa cell intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: part_of UBERON:0003729 ! mouth mucosa relationship: part_of UBERON:0003729 ! mouth mucosa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T02:51:30Z [Term] @@ -17042,7 +17062,7 @@ def: "A rounded or elliptical epithelial cell, with pale-staining open face nucl synonym: "blastema cell of olfactory epithelium" EXACT [] xref: FMA:67874 is_a: CL:0002169 ! basal cell of olfactory epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:59:18Z [Term] @@ -17053,7 +17073,7 @@ synonym: "interdental cell" EXACT [] xref: FMA:79797 is_a: CL:0002315 ! supporting cell of cochlea relationship: part_of UBERON:0002276 ! lamina of spiral limbus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:02:48Z [Term] @@ -17071,7 +17091,7 @@ is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium relationship: part_of UBERON:0002321 ! extraglomerular mesangium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:20:55Z [Term] @@ -17082,8 +17102,8 @@ xref: EMAPA:31247 xref: FMA:70589 is_a: CL:0000500 ! follicular epithelial cell is_a: CL:0002078 ! meso-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002161 NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:01:27Z [Term] @@ -17092,7 +17112,7 @@ name: primary follicular cell of ovary def: "A cell within the primary follicle of the ovary." [GOC:tfm] xref: FMA:70590 is_a: CL:0002174 ! follicular cell of ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:03:42Z [Term] @@ -17101,7 +17121,7 @@ name: secondary follicular cell of ovary def: "A cell of a secondary follicile within the ovary." [GOC:tfm] xref: FMA:70591 is_a: CL:0002174 ! follicular cell of ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:03:48Z [Term] @@ -17115,7 +17135,7 @@ is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000642 ! folliculostellate cell intersection_of: part_of UBERON:0006964 ! pars distalis of adenohypophysis relationship: part_of UBERON:0006964 ! pars distalis of adenohypophysis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:10:10Z [Term] @@ -17128,7 +17148,7 @@ is_a: CL:0002251 {is_inferred="true"} ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:22:08Z [Term] @@ -17138,7 +17158,7 @@ def: "An epithelial cell within one of the pits in the embryonic gastric mucosa subset: cellxgene_subset xref: FMA:86552 is_a: CL:0002178 ! epithelial cell of stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:23:22Z [Term] @@ -17151,7 +17171,7 @@ is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0002178 ! epithelial cell of stomach intersection_of: part_of UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0001199 ! mucosa of stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:38:51Z [Term] @@ -17167,7 +17187,7 @@ is_a: CL:0002180 {is_inferred="true"} ! mucous cell of stomach intersection_of: CL:0000651 ! mucous neck cell intersection_of: part_of UBERON:0000325 ! gastric gland relationship: part_of UBERON:0000325 ! gastric gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:41:30Z [Term] @@ -17177,7 +17197,7 @@ def: "A simple columnar cell that populates the entire luminal surface including xref: FMA:62949 is_a: CL:0000319 ! mucus secreting cell is_a: CL:0002180 ! mucous cell of stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:45:10Z [Term] @@ -17192,7 +17212,7 @@ is_a: CL:0002180 ! mucous cell of stomach intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0000325 ! gastric gland relationship: part_of UBERON:0000325 ! gastric gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:57:08Z [Term] @@ -17202,7 +17222,7 @@ def: "A flat or angular epithelial cell with condensed nuclei and darkly stainin synonym: "horizontal basal cells" EXACT [] xref: FMA:62304 is_a: CL:0002169 ! basal cell of olfactory epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:59:22Z [Term] @@ -17218,7 +17238,7 @@ is_a: CL:0011026 ! progenitor cell is_a: CL:1000428 ! stem cell of epidermis intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T03:12:49Z [Term] @@ -17229,12 +17249,12 @@ subset: cellxgene_subset subset: kidney_upper_slim xref: BTO:0004632 xref: FMA:70970 -is_a: CL:0000115 {is_inferred="true"} ! endothelial cell -is_a: CL:0000666 ! fenestrated cell -is_a: CL:1000746 ! glomerular cell +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +relationship: part_of UBERON:0000074 ! renal glomerulus +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z [Term] @@ -17244,7 +17264,7 @@ def: "A keratinocyte of the epidermis that is characterized by containing granul subset: cellxgene_subset xref: FMA:70543 is_a: CL:0000312 ! keratinocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T03:19:00Z [Term] @@ -17253,7 +17273,7 @@ name: squamous cell of epidermis def: "A flat keratinocyte immediately below the cornified layer." [GOC:tfm, ISBN:0517223651] xref: FMA:86925 is_a: CL:0000312 ! keratinocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T03:37:02Z [Term] @@ -17266,7 +17286,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T12:54:27Z [Term] @@ -17277,7 +17297,7 @@ xref: FMA:83541 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell relationship: RO:0002202 CL:0002193 ! develops from myelocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:08:15Z [Term] @@ -17291,8 +17311,8 @@ xref: FMA:83525 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell relationship: RO:0002202 CL:0000836 ! develops from promyelocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:08:19Z [Term] @@ -17304,7 +17324,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -17317,8 +17337,8 @@ is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/800" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T02:00:42Z [Term] @@ -17328,15 +17348,15 @@ alt_id: CL:1000036 def: "A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue." [PMID:17901986] subset: human_reference_atlas synonym: "hepatic oval cell" EXACT [] -synonym: "hepatic progenitor cell" EXACT [https://doi.org/10.1038/s12276-020-0483-0] {http://purl.org/dc/terms/contributor="http://orcid.org/0000-0003-1940-6740"} +synonym: "hepatic progenitor cell" EXACT [https://doi.org/10.1038/s12276-020-0483-0] {terms:contributor="http://orcid.org/0000-0003-1940-6740"} synonym: "liver progenitor cell" EXACT [https://doi.org/10.1038/s12276-020-0483-0] xref: BTO:0004270 xref: FMA:86576 is_a: CL:0011026 ! progenitor cell relationship: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 property_value: RO:0004050 "Liver progenitor cells have been variously named in rodent and human studies as oval cells, hepatic progenitor cells, liver stem cells, ductular reactions, or atypical ductular cells. They were first described as oval cells in rats due to their large nuclear-to-cytoplasm ratio and oval-shaped nuclei. On the difference between 'hepatic liver stem cells' (HLSC) and 'oval cells': \"... unlike a well-known hepatic progenitor cell population, known as oval cells in rodents, HLSCs do not express CK-7, CK-19, c-kit, CD133 and alpha-smooth muscle actin (α-SMA) (Gaudio et al., 2009)\"." xsd:string {xref="https://doi.org/10.1038/s12276-020-0483-0", xref="https://doi.org/10.3389/fcell.2021.644088"} +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T02:01:49Z [Term] @@ -17344,7 +17364,7 @@ id: CL:0002197 name: inactive chief cell of parathyoid gland def: "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1." [GOC:tfm, ISBN:0517223651] is_a: CL:0000446 ! chief cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:14:01Z [Term] @@ -17355,7 +17375,7 @@ synonym: "oxyphil" EXACT [] xref: FMA:67606 xref: MESH:D024862 is_a: CL:0002076 ! endo-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:26:49Z [Term] @@ -17365,7 +17385,7 @@ def: "An oncocyte located in the parathyroid gland." [PMID:20013317] xref: FMA:69084 is_a: CL:0002198 ! oncocyte is_a: CL:0002260 ! epithelial cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:33:23Z [Term] @@ -17379,7 +17399,7 @@ is_a: CL:0002198 ! oncocyte is_a: CL:0002257 ! epithelial cell of thyroid gland intersection_of: CL:0002198 ! oncocyte intersection_of: part_of UBERON:0002046 ! thyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:33:26Z [Term] @@ -17391,8 +17411,8 @@ subset: human_reference_atlas synonym: "type B intercalated cell" EXACT [PMID:25632105] synonym: "type B-IC" EXACT [PMID:25632105] is_a: CL:0005010 ! renal intercalated cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T01:43:55Z [Term] @@ -17403,9 +17423,9 @@ def: "An epithelial cell of the tracheobronchial tree." [GOC:tfm] xref: FMA:66816 is_a: CL:0002632 ! epithelial cell of lower respiratory tract intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: part_of UBERON:0007196 ! tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: part_of UBERON:0008397 ! tracheobronchial epithelium +relationship: part_of UBERON:0008397 ! tracheobronchial epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:09:14Z [Term] @@ -17423,7 +17443,7 @@ is_a: CL:0002253 ! epithelial cell of large intestine is_a: CL:0019032 ! intestinal tuft cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0000059 ! large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:20:50Z [Term] @@ -17437,7 +17457,7 @@ synonym: "multivesicular cell" EXACT [] synonym: "tuft cell" EXACT [] xref: FMA:67978 is_a: CL:0002076 ! endo-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:28:53Z [Term] @@ -17451,7 +17471,7 @@ is_a: CL:0002075 ! brush cell of tracheobronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:8600001 ! epithelium of lobular bronchiole relationship: part_of UBERON:8600001 ! epithelium of lobular bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:38:34Z [Term] @@ -17465,7 +17485,7 @@ is_a: CL:0002075 ! brush cell of tracheobronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001958 ! terminal bronchiole epithelium relationship: part_of UBERON:0001958 ! terminal bronchiole epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:38:36Z [Term] @@ -17481,8 +17501,8 @@ is_a: CL:0002075 {is_inferred="true"} ! brush cell of tracheobronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:38:37Z [Term] @@ -17496,8 +17516,8 @@ is_a: CL:0002075 ! brush cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:38:42Z [Term] @@ -17507,7 +17527,7 @@ def: "An epithelial cell present in the trachea and bronchi; columnar in shape; synonym: "undifferentiated columnar cell of tracheobronchial tree" EXACT [] xref: FMA:69060 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:53:59Z [Term] @@ -17518,7 +17538,7 @@ synonym: "oxidative muscle fiber" EXACT [] synonym: "red muscle fiber" EXACT [] xref: FMA:84448 is_a: CL:0008046 ! extrafusal muscle fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:20:03Z [Term] @@ -17538,7 +17558,7 @@ xref: CALOHA:TS-0940 xref: FMA:84413 is_a: CL:0000189 ! slow muscle cell is_a: CL:0002210 ! red muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:24:05Z [Term] @@ -17551,7 +17571,7 @@ synonym: "type II muscle fiber" EXACT [] xref: BTO:0001813 xref: FMA:84414 is_a: CL:0000190 ! fast muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:28:45Z [Term] @@ -17560,7 +17580,7 @@ name: white muscle cell def: "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." [GOC:tfm, ISBN:0517223651] xref: FMA:84449 is_a: CL:0000190 ! fast muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:28:48Z [Term] @@ -17576,7 +17596,7 @@ xref: BTO:0001813 xref: FMA:84415 is_a: CL:0002210 ! red muscle cell is_a: CL:0002212 ! type II muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:31:38Z [Term] @@ -17589,7 +17609,7 @@ synonym: "type IIb muscle fiber" EXACT [] xref: FMA:84416 is_a: CL:0002212 ! type II muscle cell is_a: CL:0002213 ! white muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:31:42Z [Term] @@ -17598,7 +17618,7 @@ name: intermediate muscle cell def: "An intermediate muscle cell that has characteristics of both fast and slow muscle cells." [GOC:tfm] xref: FMA:84450 is_a: CL:0008046 ! extrafusal muscle fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:51:17Z [Term] @@ -17608,7 +17628,7 @@ def: "A trophoblast that leaves the placenta and invades the endometrium and myo xref: BTO:0002366 xref: FMA:86564 is_a: CL:0000351 ! trophoblast cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:04:36Z [Term] @@ -17619,7 +17639,7 @@ comment: NOTE: currently variable immune gene segments are not represented in th synonym: "immature DEC precursor" EXACT [] synonym: "immature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T01:58:00Z [Term] @@ -17627,7 +17647,7 @@ id: CL:0002219 name: anchoring trophoblast def: "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua." [GOC:tfm, http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html] is_a: CL:0000351 ! trophoblast cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:14:28Z [Term] @@ -17636,7 +17656,7 @@ name: interstitial cell of pineal gland def: "A cell located between the pinealocytes." [GOC:tfm, ISBN:0517223651] xref: FMA:86575 is_a: CL:0000710 ! neurecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:28:41Z [Term] @@ -17646,7 +17666,7 @@ def: "A squamous cell that has keratin in the esophagus." [GOC:tfm, PMID:1169455 xref: FMA:86549 is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:11:06Z [Term] @@ -17658,7 +17678,7 @@ xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell relationship: part_of UBERON:0000965 ! lens of camera-type eye -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:38:03Z [Term] @@ -17668,7 +17688,7 @@ def: "A cell of the transparent layer of simple cuboidal epithelium over the ant subset: cellxgene_subset xref: FMA:63181 is_a: CL:0002224 ! lens epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:45:45Z [Term] @@ -17683,8 +17703,8 @@ is_a: CL:0002222 ! vertebrate lens cell intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell intersection_of: part_of UBERON:0001803 ! epithelium of lens relationship: part_of UBERON:0001803 ! epithelium of lens -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:45:47Z [Term] @@ -17697,8 +17717,8 @@ synonym: "secondary lens fibre" EXACT [] is_a: BFO:0000002 is_a: CL:0011004 ! lens fiber cell relationship: RO:0002202 CL:0002228 ! develops from primary lens fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:53:39Z [Term] @@ -17709,7 +17729,7 @@ synonym: "non-nucleated secondary lens fibre" EXACT [] xref: FMA:67561 is_a: CL:0002225 ! secondary lens fiber relationship: RO:0002202 CL:0002227 ! develops from nucleated secondary lens fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:15:23Z [Term] @@ -17719,7 +17739,7 @@ def: "A secondary fiber cell that contains a nucleus." [GOC:tfm] synonym: "nucleated secondary lens fibre" EXACT [] xref: FMA:70949 is_a: CL:0002225 ! secondary lens fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:15:26Z [Term] @@ -17732,8 +17752,8 @@ xref: FMA:70613 is_a: BFO:0000002 is_a: CL:0011004 ! lens fiber cell relationship: RO:0002202 CL:0002223 ! develops from anterior lens cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:19:01Z [Term] @@ -17742,7 +17762,7 @@ name: light chief cell of parathyroid gland def: "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules." [GOC:tfm, ISBN:0721662544] xref: FMA:69079 is_a: CL:0000446 ! chief cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:46:54Z [Term] @@ -17759,7 +17779,7 @@ is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:49:29Z [Term] @@ -17774,7 +17794,7 @@ is_a: CL:0002231 ! epithelial cell of prostate intersection_of: CL:0000072 ! non-branched duct epithelial cell intersection_of: part_of UBERON:0002485 ! prostate duct relationship: part_of UBERON:0002485 ! prostate duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:55:51Z [Term] @@ -17788,7 +17808,7 @@ is_a: CL:0002231 {is_inferred="true"} ! epithelial cell of prostate intersection_of: CL:0002231 ! epithelial cell of prostate intersection_of: part_of UBERON:0004179 ! prostate glandular acinus relationship: part_of UBERON:0004179 ! prostate glandular acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:55:53Z [Term] @@ -17802,7 +17822,7 @@ is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0002341 ! basal cell of prostate epithelium intersection_of: part_of UBERON:0004179 ! prostate glandular acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:08Z [Term] @@ -17814,7 +17834,7 @@ is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002340 ! luminal cell of prostate epithelium intersection_of: CL:0002340 ! luminal cell of prostate epithelium intersection_of: part_of UBERON:0004179 ! prostate glandular acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:10Z [Term] @@ -17829,7 +17849,7 @@ is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0002341 ! basal cell of prostate epithelium intersection_of: part_of UBERON:0002485 ! prostate duct relationship: part_of UBERON:0002485 ! prostate duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:12Z [Term] @@ -17842,7 +17862,7 @@ is_a: CL:0002340 ! luminal cell of prostate epithelium intersection_of: CL:0002340 ! luminal cell of prostate epithelium intersection_of: part_of UBERON:0002485 ! prostate duct relationship: part_of UBERON:0002485 ! prostate duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:16Z [Term] @@ -17857,7 +17877,7 @@ xref: FMA:84771 xref: VHOG:0000662 is_a: CL:0000670 ! primordial germ cell relationship: part_of UBERON:0000473 ! testis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:11:13Z [Term] @@ -17873,7 +17893,7 @@ xref: ISBN:0721662544 xref: VHOG:0000661 is_a: CL:0000670 ! primordial germ cell relationship: part_of UBERON:0000992 ! ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:11:16Z [Term] @@ -17885,7 +17905,7 @@ is_a: CL:0000057 ! fibroblast is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:25:18Z [Term] @@ -17902,7 +17922,7 @@ intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001004 ! respiratory system intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0001004 ! respiratory system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:29:38Z [Term] @@ -17914,7 +17934,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -17930,7 +17950,7 @@ intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001607 ! sphincter pupillae relationship: part_of UBERON:0001607 ! sphincter pupillae relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T08:53:42Z [Term] @@ -17941,7 +17961,7 @@ synonym: "ectocervical squamous cell" EXACT [] xref: FMA:86483 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002149 ! epithelial cell of uterus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:12:23Z [Term] @@ -17949,7 +17969,7 @@ id: CL:0002245 name: obsolete null lymphocyte def: "OBSOLETE: A lymphocyte that lacks T or B cell surface markers." [GOC:tfm, ISBN:068340007X] xref: FMA:83601 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2010-09-07T03:43:42Z @@ -17966,7 +17986,7 @@ is_a: CL:0000080 ! circulating cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000178 ! blood relationship: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:57:09Z [Term] @@ -17975,7 +17995,7 @@ name: pleural macrophage def: "A tissue macrophage that is in the pleural space." [GOC:tfm] xref: FMA:83024 is_a: CL:0000864 ! tissue-resident macrophage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T04:16:43Z [Term] @@ -17985,7 +18005,7 @@ def: "A pluripotent stem cell has the ability to form cells from all three germ xref: FMA:70570 xref: MESH:D039904 is_a: CL:0000723 ! somatic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T04:26:06Z [Term] @@ -17995,7 +18015,7 @@ def: "A stem cell that can differentiate into a cardiac myocyte." [GOC:tfm, PMID xref: FMA:75620 is_a: CL:0000035 ! single fate stem cell is_a: CL:0002078 ! meso-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T04:40:32Z [Term] @@ -18010,7 +18030,7 @@ is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:21:22Z [Term] @@ -18021,7 +18041,7 @@ is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:26:53Z [Term] @@ -18031,12 +18051,12 @@ alt_id: CL:1000402 def: "An epithelial cell of the esophagus." [GOC:tfm] subset: cellxgene_subset xref: FMA:63071 -xref: ZFA:0009400 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009400 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002251 {is_inferred="true"} ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:28:20Z [Term] @@ -18052,7 +18072,7 @@ is_a: CL:0002563 {is_inferred="true"} ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:28:22Z [Term] @@ -18066,7 +18086,7 @@ is_a: CL:0002563 {is_inferred="true"} ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:41:46Z [Term] @@ -18083,8 +18103,8 @@ intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0002337 ! endometrial stroma relationship: RO:0002388 CL:2000002 ! has potential to directly develop into decidual cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:50:04Z [Term] @@ -18095,7 +18115,7 @@ synonym: "carotid body sustentacular cell" EXACT [] xref: FMA:84188 is_a: CL:0000630 ! supporting cell is_a: CL:0000710 ! neurecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T10:34:45Z [Term] @@ -18110,7 +18130,7 @@ is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: part_of UBERON:0002046 ! thyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T01:46:51Z [Term] @@ -18125,7 +18145,7 @@ xref: BTO:0003736 xref: CALOHA:TS-1285 xref: FMA:68782 is_a: CL:0002257 ! epithelial cell of thyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T01:50:08Z [Term] @@ -18136,7 +18156,7 @@ subset: cellxgene_subset synonym: "totipotent neuroepithelial stem cell" NARROW [] xref: FMA:87171 is_a: CL:0000723 ! somatic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:14:14Z [Term] @@ -18149,7 +18169,7 @@ is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell is_a: CL:1001593 ! parathyroid glandular cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0001132 ! parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:29:38Z [Term] @@ -18159,7 +18179,7 @@ alt_id: CL:1000446 def: "An endothelial cell found in the mucosa associated with the facial skeleton." [GOC:tfm, ISBN:0618947256] xref: FMA:70627 is_a: CL:0002076 ! endo-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T10:40:12Z [Term] @@ -18170,12 +18190,12 @@ def: "An endothelial cell that lines any of the venous cavities through which bl subset: cellxgene_subset subset: human_reference_atlas xref: FMA:63134 -is_a: CL:0000115 ! endothelial cell +is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003909 ! sinusoid relationship: part_of UBERON:0003909 ! sinusoid -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T10:57:26Z [Term] @@ -18184,7 +18204,7 @@ name: transitional cell of parathyroid gland def: "One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage." [GOC:tfm, ISBN:0412046911] xref: FMA:69324 is_a: CL:0002260 ! epithelial cell of parathyroid gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:33:50Z [Term] @@ -18196,7 +18216,7 @@ is_a: CL:0002067 ! type A enteroendocrine cell is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0002067 ! type A enteroendocrine cell intersection_of: part_of UBERON:0000945 ! stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T10:54:42Z [Term] @@ -18211,7 +18231,7 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0009042 ! enteroendocrine cell of colon intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T11:37:35Z [Term] @@ -18226,7 +18246,7 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0009006 ! enteroendocrine cell of small intestine intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:34:22Z [Term] @@ -18241,7 +18261,7 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0000945 ! stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:36:03Z [Term] @@ -18252,7 +18272,7 @@ subset: cellxgene_subset xref: FMA:63418 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002269 ! vasoactive intestinal peptide secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:47:45Z [Term] @@ -18260,7 +18280,7 @@ id: CL:0002269 name: vasoactive intestinal peptide secreting cell def: "An endocrine cell that secretes vasoactive intestinal peptide." [GOC:tfm] is_a: CL:0000167 ! peptide hormone secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:52:20Z [Term] @@ -18271,7 +18291,7 @@ synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:62941 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002272 ! motilin secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:13:47Z [Term] @@ -18281,7 +18301,7 @@ def: "A type EC enteredocrine cell in the intestines that stores and secretes su xref: FMA:62940 is_a: CL:0000505 ! substance P secreting cell is_a: CL:0000577 ! type EC enteroendocrine cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:13:49Z [Term] @@ -18289,7 +18309,7 @@ id: CL:0002272 name: motilin secreting cell def: "A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect." [GOC:tfm, MESH:D009037] is_a: CL:0000167 ! peptide hormone secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:31:13Z [Term] @@ -18299,7 +18319,7 @@ def: "A type EC enteroendocrine cell type that is numerous in the fundus of the xref: FMA:63208 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002274 ! histamine secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:35:17Z [Term] @@ -18310,7 +18330,7 @@ is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion relationship: capable_of GO:0001821 ! histamine secretion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:04:42Z [Term] @@ -18326,15 +18346,15 @@ synonym: "PP-cell of pancreatic islet" EXACT [] xref: BTO:0000805 xref: FMA:70588 xref: MESH:D050418 -xref: ZFA:0005742 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005742 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000696 ! PP cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0000696 ! PP cell intersection_of: part_of UBERON:0000006 ! islet of Langerhans intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:30:31Z [Term] @@ -18343,7 +18363,7 @@ name: obsolete PP cell of pancreatic acinus def: "OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus." [GOC:tfm] synonym: "type F cell of pancreatic acinus" EXACT [] xref: FMA:85400 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2010-09-10T03:30:33Z @@ -18356,7 +18376,7 @@ synonym: "CCK cell" EXACT [] xref: FMA:62937 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:44:36Z [Term] @@ -18368,7 +18388,7 @@ synonym: "type K enteroendocrine cell" EXACT [] xref: FMA:62942 is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0009006 ! enteroendocrine cell of small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:51:47Z [Term] @@ -18379,7 +18399,7 @@ subset: cellxgene_subset xref: FMA:62944 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:59:09Z [Term] @@ -18391,7 +18411,7 @@ synonym: "N cell" EXACT [] xref: FMA:62943 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T04:08:29Z [Term] @@ -18402,7 +18422,7 @@ xref: FMA:62936 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0000458 ! serotonin secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T04:44:46Z [Term] @@ -18412,7 +18432,7 @@ def: "An enteroendocrine cell which produces a gastrin- and cholecystokinin-like xref: FMA:63421 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000509 ! gastrin secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T09:48:34Z [Term] @@ -18422,7 +18442,7 @@ alt_id: CL:1000440 def: "An epithelial cell of the mucosa associated with facial skeleton." [GOC:tfm, ISBN:0323052908] xref: FMA:70581 is_a: CL:0002159 ! general ecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T11:04:02Z [Term] @@ -18434,7 +18454,7 @@ synonym: "X/A-like" EXACT [] xref: FMA:63209 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0005018 ! ghrelin secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:12:12Z [Term] @@ -18446,7 +18466,7 @@ synonym: "type 3 taste cell" EXACT [] xref: FMA:67940 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000209 ! taste receptor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:21Z [Term] @@ -18456,7 +18476,7 @@ def: "A taste receptor cell that has a short microvilli, a projecting apical reg synonym: "type 2 taste cell" EXACT [] xref: FMA:62381 is_a: CL:0000209 ! taste receptor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:26Z [Term] @@ -18469,7 +18489,7 @@ synonym: "type 4 taste cell" EXACT [] xref: FMA:62380 is_a: CL:0000034 ! stem cell is_a: CL:0000209 ! taste receptor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:29Z [Term] @@ -18478,7 +18498,7 @@ name: type V taste receptor cell def: "A cell type that forms the boundary with the surrounding epithelium." [GOC:tfm, ISBN:0517223651] xref: FMA:67941 is_a: CL:0000209 ! taste receptor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:31Z [Term] @@ -18491,7 +18511,7 @@ synonym: "type taste 1 cell" EXACT [] xref: FMA:62356 is_a: CL:0000209 ! taste receptor cell is_a: CL:0000703 ! sustentacular cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:35Z [Term] @@ -18502,7 +18522,7 @@ synonym: "Y bearing sperm" EXACT [] synonym: "Y-bearing sperm" EXACT [] xref: FMA:84058 is_a: CL:0000019 ! sperm -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T11:35:24Z [Term] @@ -18513,7 +18533,7 @@ synonym: "X bearing sperm" EXACT [] synonym: "X-bearing sperm" EXACT [] xref: FMA:84057 is_a: CL:0000019 ! sperm -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T11:35:26Z [Term] @@ -18524,8 +18544,8 @@ subset: human_reference_atlas synonym: "glomus cell" EXACT [] xref: FMA:84186 is_a: CL:0000710 ! neurecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T01:40:21Z [Term] @@ -18544,7 +18564,7 @@ is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002370 ! thymus relationship: part_of UBERON:0002370 ! thymus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:34:22Z [Term] @@ -18554,7 +18574,7 @@ def: "An epithelial cell with a well defined Golgi apparatus that makes up the c synonym: "subcapsular thymic epithelial cell" RELATED [PMID:18194204, PMID:2694455] xref: FMA:72209 is_a: CL:0002364 ! cortical thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:23Z [Term] @@ -18566,7 +18586,7 @@ synonym: "large medullary thymic epithelial cells" EXACT [] synonym: "large mTEC" EXACT [] xref: FMA:72214 is_a: CL:0002365 ! medullary thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:26Z [Term] @@ -18577,7 +18597,7 @@ synonym: "dark thymic epithelial cell" EXACT [] xref: FMA:72212 is_a: CL:0002364 ! cortical thymic epithelial cell is_a: CL:0002365 ! medullary thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:45Z [Term] @@ -18587,7 +18607,7 @@ def: "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-de synonym: "intermediate thymic epithelial cell" EXACT [] xref: FMA:72211 is_a: CL:0002364 ! cortical thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:51Z [Term] @@ -18599,7 +18619,7 @@ synonym: "undifferentiated mTEC" EXACT [] synonym: "undifferentiated thymic epithelial cell" EXACT [] xref: FMA:72213 is_a: CL:0002365 ! medullary thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:54Z [Term] @@ -18609,7 +18629,7 @@ def: "An epithelial cell scattered in the cortex, predominant in the outer corte synonym: "pale thymic epithelial cell" EXACT [] xref: FMA:72210 is_a: CL:0002364 ! cortical thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:58Z [Term] @@ -18619,13 +18639,13 @@ def: "A small medullary thymic epithelial cell with a spindle shape, often arran synonym: "spindle shaped medullary thymic epithelial cell" EXACT [] synonym: "spindle shaped mTEC" EXACT [] is_a: CL:0002365 ! medullary thymic epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:23:25Z [Term] id: CL:0002301 name: type B synovial cell -def: "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." [GOC:tfm, ISBN:0517223651, PMID:34433485, PMID:34772990] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} +def: "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." [GOC:tfm, ISBN:0517223651, PMID:34433485, PMID:34772990] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} comment: Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. {xref="https://en.wikipedia.org/wiki/Fibroblast-like_synoviocyte", xref="PMID:34433485"} synonym: "fibroblast-like synoviocyte" EXACT [] synonym: "synovial fibroblast" EXACT [PMID:23147896] @@ -18638,7 +18658,7 @@ intersection_of: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: capable_of GO:0030213 ! hyaluronan biosynthetic process relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: produces UBERON:0001090 ! synovial fluid -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:39:14Z [Term] @@ -18652,7 +18672,7 @@ is_a: CL:0000214 ! synovial cell is_a: CL:0000234 ! phagocyte relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: RO:0001000 CL:0000842 {xref="PMID:10770586"} ! derives from mononuclear cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:39:17Z [Term] @@ -18667,8 +18687,8 @@ synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T04:09:27Z [Term] @@ -18684,8 +18704,8 @@ synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T04:09:31Z [Term] @@ -18707,13 +18727,13 @@ relationship: part_of UBERON:0004135 ! distal tubule id: CL:0002306 name: epithelial cell of proximal tubule def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1-4160-2328-3] +comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. subset: cellxgene_subset subset: human_reference_atlas subset: kidney_upper_slim synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:70973 xref: KUPO:0001044 -is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell @@ -18725,9 +18745,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0002307 name: brush border cell of the proximal tubule -def: "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow." [GOC:tfm, ISBN:1-4160-2328-3] +def: "A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste." [GOC:tfm, ISBN:1-4160-2328-3, PMID:23799132] +comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. +is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0002306 ! epithelial cell of proximal tubule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: CL:0002306 ! epithelial cell of proximal tubule +intersection_of: has_part GO:0005903 ! brush border +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T11:29:20Z [Term] @@ -18740,7 +18764,7 @@ is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002419 ! skin gland relationship: part_of UBERON:0002419 ! skin gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T12:00:07Z [Term] @@ -18752,7 +18776,7 @@ xref: FMA:83098 xref: MESH:D052680 is_a: CL:0000467 ! adrenocorticotropic hormone secreting cell is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:08:23Z [Term] @@ -18763,7 +18787,7 @@ xref: FMA:83097 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000439 ! prolactin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:25:34Z [Term] @@ -18780,7 +18804,7 @@ synonym: "mammotropic cell" EXACT [] xref: FMA:83096 is_a: CL:0000439 ! prolactin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:30:57Z [Term] @@ -18794,7 +18818,7 @@ xref: FMA:83095 xref: MESH:D052683 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:33:09Z [Term] @@ -18813,7 +18837,7 @@ intersection_of: capable_of GO:0046879 ! hormone secretion intersection_of: part_of UBERON:0002367 ! prostate gland relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0002367 ! prostate gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:01:58Z [Term] @@ -18822,7 +18846,7 @@ name: external supporting cell of vestibular epithelium def: "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein." [GOC:tfm, PMID:20837532] xref: FMA:75809 is_a: CL:0002316 ! supporting cell of vestibular epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:20:01Z [Term] @@ -18835,7 +18859,7 @@ is_a: CL:0005014 ! auditory epithelial supporting cell intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0001844 ! cochlea relationship: part_of UBERON:0001844 ! cochlea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:31:38Z [Term] @@ -18847,7 +18871,7 @@ is_a: CL:0005014 ! auditory epithelial supporting cell intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0001862 ! vestibular labyrinth relationship: part_of UBERON:0001862 ! vestibular labyrinth -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:31:44Z [Term] @@ -18856,7 +18880,7 @@ name: external limiting cell of vestibular epithelium def: "An external limiting cell found in the vestibular epithelium." [GOC:tfm] xref: FMA:75808 is_a: CL:0002316 ! supporting cell of vestibular epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:33:50Z [Term] @@ -18867,7 +18891,7 @@ xref: FMA:86712 is_a: BFO:0000002 is_a: CL:0000081 ! blood cell relationship: RO:0002202 CL:0000077 ! develops from mesothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T10:47:11Z [Term] @@ -18881,7 +18905,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -18893,12 +18917,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -18908,9 +18932,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -18926,7 +18950,7 @@ xref: FMA:82841 xref: MESH:D053595 is_a: CL:0000034 ! stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:44:35Z [Term] @@ -18938,7 +18962,7 @@ is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell intersection_of: CL:0000349 ! extraembryonic cell intersection_of: RO:0001025 UBERON:0000173 ! located in amniotic fluid relationship: RO:0001025 UBERON:0000173 ! located in amniotic fluid -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T10:13:37Z [Term] @@ -18961,9 +18985,9 @@ is_a: CL:0000185 ! myoepithelial cell is_a: CL:0002327 ! mammary gland epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4969-670X +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-4969-670X creation_date: 2010-09-20T11:42:14Z [Term] @@ -18990,9 +19014,9 @@ intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0003214 ! mammary gland alveolus relationship: part_of UBERON:0003214 ! mammary gland alveolus relationship: RO:0002202 CL:4033057 ! develops from luminal adaptive secretory precursor cell of mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4361-817X +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-4361-817X creation_date: 2010-09-20T01:30:57Z [Term] @@ -19006,7 +19030,7 @@ is_a: BFO:0000002 is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:0002327 ! mammary gland epithelial cell relationship: RO:0002202 CL:0009116 ! develops from progenitor cell of mammary luminal epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T01:37:53Z [Term] @@ -19021,7 +19045,7 @@ is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T01:49:37Z [Term] @@ -19034,7 +19058,7 @@ is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:00:00Z [Term] @@ -19044,8 +19068,8 @@ def: "An epithelial cell type that lacks the columnar shape typical for other re subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0002202 ! epithelial cell of tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:10:36Z [Term] @@ -19053,7 +19077,7 @@ id: CL:0002330 name: undifferentiated cell of bronchus epithelium def: "An undifferentiated columnar cell of the bronchus epithelium" [GOC:tfm, PMID:18757316] is_a: CL:0002328 ! bronchial epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:17:58Z [Term] @@ -19066,8 +19090,8 @@ is_a: CL:0002145 ! ciliated columnar cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:0002185 ! bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:21:12Z [Term] @@ -19078,7 +19102,7 @@ is_a: CL:0000136 ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell relationship: RO:0002202 CL:0000005 ! develops from neural crest derived fibroblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:25:25Z [Term] @@ -19087,7 +19111,7 @@ name: preadipocyte def: "An undifferentiated fibroblast that can be stimulated to form a fat cell." [GOC:tfm, PMID:18793119] xref: BTO:0001107 is_a: CL:0000057 ! fibroblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:31:53Z [Term] @@ -19095,7 +19119,7 @@ id: CL:0002335 name: brown preadipocyte def: "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)." [GOC:tfm, PMID:18719589] is_a: CL:0002334 ! preadipocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:38:38Z [Term] @@ -19103,7 +19127,7 @@ id: CL:0002336 name: buccal mucosa cell def: "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek." [GOC:tfm, MESH:D009061] is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:52:54Z [Term] @@ -19116,8 +19140,8 @@ synonym: "bulge keratinocyte" EXACT [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000312 ! keratinocyte is_a: CL:0011026 ! progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:07:03Z [Term] @@ -19142,7 +19166,7 @@ relationship: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like prot relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002202 CL:0002344 ! develops from CD56-negative, CD161-positive immature natural killer cell, human -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:06:53Z [Term] @@ -19154,7 +19178,7 @@ is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0002367 ! prostate gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:21:06Z [Term] @@ -19164,8 +19188,8 @@ def: "The exocrine cell of the prostate, this epithelial cell secretes prostatic subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0002231 ! epithelial cell of prostate -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:34:05Z [Term] @@ -19175,8 +19199,8 @@ def: "An undifferentiated cell of the prostate epithelium that lacks secretory a subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0002231 ! epithelial cell of prostate -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:34:10Z [Term] @@ -19184,7 +19208,7 @@ id: CL:0002342 name: circulating endothelial cell def: "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage." [GOC:tfm, PMID:19652886] is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:49:58Z [Term] @@ -19205,8 +19229,8 @@ relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity relationship: RO:0002104 PR:000009766 ! has plasma membrane part galectin-1 relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T04:00:02Z [Term] @@ -19229,7 +19253,7 @@ relationship: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 r relationship: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T04:33:11Z [Term] @@ -19253,7 +19277,7 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002202 CL:0002346 ! develops from Dx5-negative, NK1.1-positive immature natural killer cell, mouse relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001963 ! has low plasma membrane amount CD27 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T04:41:01Z [Term] @@ -19268,7 +19292,7 @@ intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000001008 ! lacks_plasma_membrane_part integrin alpha-2 relationship: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:11:44Z [Term] @@ -19285,7 +19309,7 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002202 CL:0002349 ! develops from CD27-high, CD11b-low natural killer cell, mouse relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:19:49Z [Term] @@ -19301,7 +19325,7 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002202 CL:0002347 ! develops from CD27-high, CD11b-high natural killer cell, mouse relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001963 ! has low plasma membrane amount CD27 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:19:54Z [Term] @@ -19317,7 +19341,7 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002202 CL:0002345 ! develops from CD27-low, CD11b-low immature natural killer cell, mouse relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:20:00Z [Term] @@ -19334,8 +19358,8 @@ is_a: CL:0010008 ! cardiac endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002165 ! endocardium relationship: part_of UBERON:0002165 ! endocardium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T04:33:05Z [Term] @@ -19346,7 +19370,7 @@ subset: cellxgene_subset synonym: "pancreatic endocrine progenitor" EXACT [] synonym: "pancreatic islet progenitor cell" EXACT [] is_a: CL:0011026 ! progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T04:41:06Z [Term] @@ -19357,7 +19381,7 @@ is_a: CL:0000037 ! hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:05:13Z [Term] @@ -19383,7 +19407,7 @@ relationship: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family mem relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:08:32Z [Term] @@ -19406,7 +19430,7 @@ relationship: part_of UBERON:0001040 ! yolk sac relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:08:34Z [Term] @@ -19428,7 +19452,7 @@ relationship: has_part PR:000008467 ! hemoglobin subunit zeta relationship: has_part PR:000008857 ! hemoglobin subunit beta-1 relationship: part_of UBERON:0000922 ! embryo relationship: RO:0002202 CL:0002361 ! develops from primitive erythroid progenitor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:27:05Z [Term] @@ -19442,7 +19466,7 @@ intersection_of: bearer_of PATO:0000586 ! increased size intersection_of: RO:0002202 CL:0002355 ! develops from primitive red blood cell relationship: bearer_of PATO:0000586 ! increased size relationship: RO:0002202 CL:0002355 ! develops from primitive red blood cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:35:16Z [Term] @@ -19457,7 +19481,7 @@ intersection_of: part_of UBERON:0000922 ! embryo relationship: has_part PR:000008857 ! hemoglobin subunit beta-1 relationship: part_of UBERON:0000922 ! embryo relationship: RO:0002202 CL:0002353 ! develops from fetal liver hematopoietic progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:38:32Z [Term] @@ -19470,7 +19494,7 @@ intersection_of: bearer_of PATO:0000587 ! decreased size intersection_of: RO:0002202 CL:0002355 ! develops from primitive red blood cell relationship: bearer_of PATO:0000587 ! decreased size relationship: RO:0002202 CL:0002355 ! develops from primitive red blood cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:02:37Z [Term] @@ -19481,7 +19505,7 @@ is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:30:02Z [Term] @@ -19489,7 +19513,7 @@ id: CL:0002360 name: AGM hematopoietic stem cell def: "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC." [GOC:tfm, ISBN:978-1-60327-346-6] is_a: CL:0002352 ! gestational hematopoietic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:31:49Z [Term] @@ -19503,7 +19527,7 @@ intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002202 CL:0002418 ! develops from hemangioblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:47:28Z [Term] @@ -19516,7 +19540,7 @@ synonym: "granule cell progenitor" BROAD [doi:10.3389/fncir.2020.611841] is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0002319 ! neural cell relationship: part_of UBERON:0009841 ! upper rhombic lip -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T01:40:44Z [Term] @@ -19532,8 +19556,8 @@ is_a: CL:0000005 ! neural crest derived fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T01:57:40Z [Term] @@ -19548,8 +19572,8 @@ is_a: CL:0002293 ! epithelial cell of thymus intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002123 ! cortex of thymus relationship: part_of UBERON:0002123 ! cortex of thymus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T03:17:12Z [Term] @@ -19563,7 +19587,7 @@ is_a: CL:0002293 ! epithelial cell of thymus intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002124 ! medulla of thymus relationship: part_of UBERON:0002124 ! medulla of thymus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T03:17:14Z [Term] @@ -19577,7 +19601,7 @@ is_a: CL:0002601 ! uterine smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001296 ! myometrium relationship: part_of UBERON:0001296 ! myometrium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T03:46:34Z [Term] @@ -19589,7 +19613,7 @@ is_a: CL:0000115 {is_inferred="true"} ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0005969 ! eye trabecular meshwork relationship: part_of UBERON:0005969 ! eye trabecular meshwork -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T04:18:50Z [Term] @@ -19599,11 +19623,11 @@ def: "An endo-epithelial cell of the respiratory tract." [GOC:tfm] subset: cellxgene_subset synonym: "airway epithelial cell" EXACT [] xref: BTO:0004533 -is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell -intersection_of: CL:0002076 ! endo-epithelial cell -intersection_of: part_of UBERON:0000065 ! respiratory tract -relationship: part_of UBERON:0000065 ! respiratory tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +is_a: CL:0002076 ! endo-epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium +relationship: part_of UBERON:0004802 ! respiratory tract epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T04:38:49Z [Term] @@ -19612,7 +19636,7 @@ name: fungal spore def: "A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions." [FAO:0000019, GOC:tfm] xref: MESH:D013172 is_a: CL:0000521 ! fungal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:02:42Z [Term] @@ -19622,10 +19646,10 @@ def: "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic r subset: cellxgene_subset synonym: "respiratory mucosa goblet cells" EXACT [MP:0010863] is_a: CL:0000160 ! goblet cell +is_a: CL:0002368 ! respiratory epithelial cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0000065 ! respiratory tract -relationship: part_of UBERON:0004802 ! respiratory tract epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T04:42:27Z [Term] @@ -19638,7 +19662,7 @@ xref: BTO:0001268 xref: FMA:72300 xref: WBbt:0008378 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1150 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true replaced_by: CL:0000000 creation_date: 2010-09-24T09:44:42Z @@ -19650,7 +19674,7 @@ alt_id: CL:0000369 def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] synonym: "myotubule" EXACT [] synonym: "single cell sarcomere" EXACT [] -xref: FBbt:00005812 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000187 ! muscle cell @@ -19658,7 +19682,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere relationship: bearer_of PATO:0002478 ! transversely striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:13:01Z [Term] @@ -19668,7 +19692,7 @@ def: "A peptide hormone secreting cell that secretes growth hormone releasing ho synonym: "GHRH secreting cell" EXACT [] synonym: "somatocrinin secreting cell" EXACT [] is_a: CL:0000167 ! peptide hormone secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:36:44Z [Term] @@ -19681,19 +19705,19 @@ is_a: CL:0000855 ! sensory hair cell intersection_of: CL:0000855 ! sensory hair cell intersection_of: part_of UBERON:0001690 ! ear relationship: part_of UBERON:0001690 ! ear -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:49:31Z [Term] id: CL:0002375 name: Schwann cell precursor -def: "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19." [GOC:tfm] +def: "A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19." [GOC:tfm] subset: cellxgene_subset synonym: "Schwann cell precursor cell" EXACT [] is_a: CL:0000030 ! glioblast is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:06:10Z [Term] @@ -19703,7 +19727,7 @@ def: "A glial cell that ensheaths multiple small diameter axons in the periphera synonym: "Schwann cell" BROAD [] is_a: CL:0002573 ! Schwann cell relationship: RO:0002202 CL:0002377 ! develops from immature Schwann cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:10:26Z [Term] @@ -19712,10 +19736,10 @@ name: immature Schwann cell def: "A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons." [GOC:cvs, GOC:tfm, ISBN:0721662544] subset: cellxgene_subset synonym: "Schwann cell" BROAD [] -xref: ZFA:0001725 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0001725 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002573 ! Schwann cell relationship: RO:0002202 CL:0002375 ! develops from Schwann cell precursor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:10:31Z [Term] @@ -19725,7 +19749,7 @@ def: "A double negative thymocyte that has a T cell receptor consisting of a gam comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "fetal Vgamma2+ thymocyte" BROAD [] is_a: CL:0002404 ! fetal thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:21:07Z [Term] @@ -19735,7 +19759,7 @@ def: "A neurecto-epithelial cell found in the arachnoid villi of dura mater. Thi synonym: "arachnoid cap cell" EXACT [] xref: FMA:86588 is_a: CL:0000710 ! neurecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-28T02:23:46Z [Term] @@ -19744,7 +19768,7 @@ name: oospore def: "An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere." [GOC:tfm, ISBN:0851988857, SGD:clt] xref: FAO:0000039 is_a: CL:0000605 ! fungal asexual spore -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:22:45Z [Term] @@ -19753,7 +19777,7 @@ name: uninucleate conidium def: "A conidium that has only one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000025 is_a: CL:0000599 ! conidium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:26:39Z [Term] @@ -19762,7 +19786,7 @@ name: multinucleate conidium def: "A conidium that has more than one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000033 is_a: CL:0000599 ! conidium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:31:28Z [Term] @@ -19862,7 +19886,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001199 ! lacks_plasma_membrane_part C-C chemokine receptor type 2 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: RO:0002202 CL:0000860 ! develops from classical monocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T10:52:03Z [Term] @@ -19882,8 +19906,8 @@ intersection_of: RO:0002104 PR:000002105 ! has plasma membrane part thrombomodul relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0042590 ! antigen processing and presentation of exogenous peptide antigen via MHC class I relationship: RO:0002104 PR:000002105 ! has plasma membrane part thrombomodulin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T02:38:58Z [Term] @@ -19904,7 +19928,7 @@ relationship: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type relationship: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 relationship: CL:4030046 PR:000001879 ! lacks_plasma_membrane_part leukosialin relationship: RO:0015015 PR:000002980 ! has high plasma membrane amount lymphocyte antigen 6C2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T11:26:18Z [Term] @@ -19923,8 +19947,8 @@ intersection_of: RO:0015016 PR:000001889 ! has low plasma membrane amount CD14 m relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III relationship: RO:0002202 CL:0002397 ! develops from CD14-positive, CD16-positive monocyte relationship: RO:0015016 PR:000001889 ! has low plasma membrane amount CD14 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T12:25:42Z [Term] @@ -19940,7 +19964,7 @@ intersection_of: CL:4030046 PR:000001199 ! lacks_plasma_membrane_part C-C chemok intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III relationship: CL:4030046 PR:000001199 ! lacks_plasma_membrane_part C-C chemokine receptor type 2 relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T12:49:47Z [Term] @@ -19957,7 +19981,7 @@ intersection_of: RO:0002104 PR:000002980 ! has plasma membrane part lymphocyte a relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000002980 ! has plasma membrane part lymphocyte antigen 6C2 relationship: RO:0002202 CL:0002395 ! develops from Gr1-high classical monocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T12:49:49Z [Term] @@ -19973,8 +19997,8 @@ intersection_of: capable_of GO:0032637 ! interleukin-8 production intersection_of: RO:0002104 PR:000002027 ! has plasma membrane part T-cell surface glycoprotein CD1c relationship: capable_of GO:0032637 ! interleukin-8 production relationship: RO:0002104 PR:000002027 ! has plasma membrane part T-cell surface glycoprotein CD1c -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T02:39:01Z [Term] @@ -19991,7 +20015,7 @@ intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement c relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-05T10:11:38Z [Term] @@ -20003,7 +20027,7 @@ synonym: "mature DEC precursor" EXACT [] synonym: "mature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte relationship: RO:0002202 CL:0002218 ! develops from immature dendritic epithelial T cell precursor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:05:46Z [Term] @@ -20027,7 +20051,7 @@ relationship: CL:4030046 PR:000002037 ! lacks_plasma_membrane_part complement co relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-05T11:18:03Z [Term] @@ -20038,7 +20062,7 @@ comment: NOTE: currently variable immune gene segments are not represented in th synonym: "fetal Vgamma2-positive" EXACT [] is_a: CL:0002404 ! fetal thymocyte relationship: RO:0002202 CL:0002378 ! develops from immature Vgamma2-positive fetal thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:24:36Z [Term] @@ -20046,7 +20070,7 @@ id: CL:0002404 name: fetal thymocyte def: "A thymocyte found in the fetal thymus." [GOC:tfm] is_a: CL:0000893 ! thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:28:25Z [Term] @@ -20061,7 +20085,7 @@ intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:33:39Z [Term] @@ -20071,7 +20095,7 @@ def: "A double negative post-natal thymocyte that has a T cell receptor consisti comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-positive thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:53:44Z [Term] @@ -20082,7 +20106,7 @@ comment: NOTE: currently variable immune gene segments are not represented in th synonym: "Vgamma2-positive" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte relationship: RO:0002202 CL:0002406 ! develops from immature Vgamma2-positive thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:53:48Z [Term] @@ -20092,7 +20116,7 @@ def: "A double negative post-natal thymocyte that has a T cell receptor consisti comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-negative thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:59:05Z [Term] @@ -20103,7 +20127,7 @@ comment: NOTE: currently variable immune gene segments are not represented in th synonym: "Vgamma2-negative" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte relationship: RO:0002202 CL:0002408 ! develops from immature Vgamma2-negative thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:59:08Z [Term] @@ -20117,8 +20141,8 @@ synonym: "PaSC" EXACT [] xref: MESH:D058954 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0001264 ! pancreas -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T09:40:33Z [Term] @@ -20127,7 +20151,7 @@ name: Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Vg1.1-positive, Vd6.3-negative T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:07:44Z [Term] @@ -20136,7 +20160,7 @@ name: Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:03:00Z [Term] @@ -20145,7 +20169,7 @@ name: mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org] synonym: "mature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:32Z [Term] @@ -20154,7 +20178,7 @@ name: immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "immature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:35Z [Term] @@ -20163,7 +20187,7 @@ name: immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "immature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:39Z [Term] @@ -20172,7 +20196,7 @@ name: mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "mature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:41Z [Term] @@ -20180,7 +20204,7 @@ id: CL:0002417 name: primitive erythroid lineage cell def: "An immature or mature cell of the first erythroid lineage to arise during embryonic development." [GOC:tfm] is_a: CL:0000764 ! erythroid lineage cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T11:22:41Z [Term] @@ -20191,7 +20215,7 @@ xref: MESH:D055018 is_a: BFO:0000002 is_a: CL:0000222 ! mesodermal cell relationship: RO:0002202 CL:0002354 ! develops from yolk sac hematopoietic stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T12:21:16Z [Term] @@ -20208,7 +20232,7 @@ intersection_of: output_of GO:0045058 ! T cell selection intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex relationship: output_of GO:0045058 ! T cell selection relationship: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:15Z [Term] @@ -20224,7 +20248,7 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0045058 ! has_not_completed T cell selection -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:17Z [Term] @@ -20235,7 +20259,7 @@ is_a: CL:0000558 {is_inferred="true"} ! reticulocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000558 ! reticulocyte intersection_of: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-15T09:24:05Z [Term] @@ -20251,7 +20275,7 @@ intersection_of: CL:0000558 ! reticulocyte intersection_of: bearer_of PATO:0001405 ! anucleate intersection_of: has_part GO:0005840 ! ribosome relationship: has_part GO:0005840 ! ribosome -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-15T09:24:08Z [Term] @@ -20263,7 +20287,7 @@ is_a: CL:0000806 {is_inferred="true"} ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T10:12:05Z [Term] @@ -20276,7 +20300,7 @@ intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0002202 CL:0002423 ! develops from DN2a thymocyte relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T10:12:08Z [Term] @@ -20298,8 +20322,8 @@ relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T01:16:24Z [Term] @@ -20314,7 +20338,7 @@ intersection_of: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecul intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:07:59Z [Term] @@ -20326,7 +20350,7 @@ is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: bearer_of PATO:0000587 ! decreased size relationship: bearer_of PATO:0000587 ! decreased size -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T01:59:06Z [Term] @@ -20342,7 +20366,7 @@ intersection_of: participates_in GO:0008283 ! cell population proliferation relationship: bearer_of PATO:0000586 ! increased size relationship: participates_in GO:0008283 ! cell population proliferation relationship: RO:0002202 CL:0002427 ! develops from resting double-positive thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T01:59:11Z [Term] @@ -20359,7 +20383,7 @@ relationship: participates_in GO:0043368 ! positive T cell selection relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002202 CL:0002428 ! develops from double-positive blast relationship: RO:0015016 GO:0042105 ! has low plasma membrane amount alpha-beta T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:11:52Z [Term] @@ -20379,7 +20403,7 @@ relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002202 CL:0002429 ! develops from CD69-positive double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000001004 ! has low plasma membrane amount CD4 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:29:19Z [Term] @@ -20399,7 +20423,7 @@ relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002202 CL:0002429 ! develops from CD69-positive double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000025402 ! has low plasma membrane amount T cell receptor co-receptor CD8 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:29:23Z [Term] @@ -20416,7 +20440,7 @@ intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-b relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002202 CL:0002433 ! develops from CD69-positive, CD4-positive single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:43:52Z [Term] @@ -20432,7 +20456,7 @@ intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-b relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002202 CL:0002431 ! develops from CD4-positive, CD8-intermediate double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:46:02Z [Term] @@ -20449,7 +20473,7 @@ intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-b relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002202 CL:0002435 ! develops from CD69-positive, CD8-positive single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:59:10Z [Term] @@ -20465,7 +20489,7 @@ intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-b relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002202 CL:0002430 ! develops from CD4-intermediate, CD8-positive double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:59:14Z [Term] @@ -20481,8 +20505,8 @@ intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal relationship: RO:0002202 CL:0002432 ! develops from CD24-positive, CD4 single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T03:31:19Z [Term] @@ -20498,8 +20522,8 @@ intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal relationship: RO:0002202 CL:0002434 ! develops from CD24-positive, CD8 single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T03:51:50Z [Term] @@ -20515,7 +20539,7 @@ intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:18:04Z [Term] @@ -20528,7 +20552,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000002023 ! has plasma membrane part NKG2-A/NKG2-B type II integral membrane protein intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000002023 ! has plasma membrane part NKG2-A/NKG2-B type II integral membrane protein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:31:09Z [Term] @@ -20541,7 +20565,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000009619 ! has plasma membrane part killer cell lectin-like receptor 4 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000009619 ! has plasma membrane part killer cell lectin-like receptor 4 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:19Z [Term] @@ -20554,7 +20578,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000001402 ! has plasma membrane part killer cell lectin-like receptor subfamily D member 1 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000001402 ! has plasma membrane part killer cell lectin-like receptor subfamily D member 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:28Z [Term] @@ -20571,7 +20595,7 @@ intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 relationship: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:56:21Z [Term] @@ -20585,7 +20609,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000009618 ! has plasma membrane part killer cell lectin-like receptor 3 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000009618 ! has plasma membrane part killer cell lectin-like receptor 3 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:38Z [Term] @@ -20598,7 +20622,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000009623 ! has plasma membrane part killer cell lectin-like receptor 8 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000009623 ! has plasma membrane part killer cell lectin-like receptor 8 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:43Z [Term] @@ -20611,7 +20635,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000009619 ! lacks_plasma_membrane_part killer cell lectin-like receptor 4 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000009619 ! lacks_plasma_membrane_part killer cell lectin-like receptor 4 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:39:02Z [Term] @@ -20625,7 +20649,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:52:04Z [Term] @@ -20638,7 +20662,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:54:18Z [Term] @@ -20651,7 +20675,7 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000009623 ! lacks_plasma_membrane_part killer cell lectin-like receptor 8 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000009623 ! lacks_plasma_membrane_part killer cell lectin-like receptor 8 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:42:42Z [Term] @@ -20665,16 +20689,16 @@ intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: RO:0002104 PR:000001402 ! has plasma membrane part killer cell lectin-like receptor subfamily D member 1 intersection_of: RO:0002104 PR:000009618 ! has plasma membrane part killer cell lectin-like receptor 3 intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:56:27Z [Term] id: CL:0002450 name: tether cell def: "A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place." [GOC:cvs, GOC:tfm, PMID:9398434] -xref: ZFA:0005565 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005565 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002374 ! ear hair cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T01:41:00Z [Term] @@ -20682,7 +20706,7 @@ id: CL:0002451 name: mammary stem cell def: "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." [GOC:hjd, GOC:tfm, PMID:15987436, PMID:16397499, PMID:17851544] is_a: CL:0000048 ! multi fate stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T01:46:51Z [Term] @@ -20695,12 +20719,12 @@ subset: human_reference_atlas synonym: "O-2A/OPC" RELATED OMO:0003000 [PMID:24133281] synonym: "O2A/OPC" RELATED OMO:0003000 [PMID:11756508] synonym: "oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell" BROAD [PMID:2253328] -synonym: "oligodendrocyte/type-2 astrocyte progenitor cell" BROAD [PMID:24133281] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} +synonym: "oligodendrocyte/type-2 astrocyte progenitor cell" BROAD [PMID:24133281] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} xref: MESH:D000073637 is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T02:51:34Z [Term] @@ -20715,7 +20739,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T01:10:28Z [Term] @@ -20729,7 +20753,7 @@ intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell sur intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T01:27:37Z [Term] @@ -20743,7 +20767,7 @@ intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T01:23:07Z [Term] @@ -20762,8 +20786,8 @@ intersection_of: RO:0002104 PR:000001014 ! has plasma membrane part receptor-typ relationship: RO:0001025 UBERON:0001003 ! located in skin epidermis relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T03:57:57Z [Term] @@ -20774,7 +20798,7 @@ is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T04:06:22Z [Term] @@ -20786,7 +20810,7 @@ intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T04:09:44Z [Term] @@ -20799,8 +20823,8 @@ is_a: CL:0000941 {is_inferred="true"} ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T10:58:53Z [Term] @@ -20813,7 +20837,7 @@ intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E relationship: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:32:43Z [Term] @@ -20829,7 +20853,7 @@ intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 relationship: part_of UBERON:0001013 ! adipose tissue relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:38:21Z [Term] @@ -20841,7 +20865,7 @@ is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 relationship: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:40:44Z [Term] @@ -20853,7 +20877,7 @@ is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001968 ! lacks_plasma_membrane_part tyrosine-protein phosphatase non-receptor type substrate 1 relationship: CL:4030046 PR:000001968 ! lacks_plasma_membrane_part tyrosine-protein phosphatase non-receptor type substrate 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:40:46Z [Term] @@ -20864,7 +20888,7 @@ is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:50:05Z [Term] @@ -20882,7 +20906,7 @@ relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alph relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015016 PR:000001013 ! has low plasma membrane amount integrin alpha-X -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:00:21Z [Term] @@ -20896,7 +20920,7 @@ intersection_of: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin a intersection_of: RO:0015015 PR:000002980 ! has high plasma membrane amount lymphocyte antigen 6C2 relationship: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X relationship: RO:0015015 PR:000002980 ! has high plasma membrane amount lymphocyte antigen 6C2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:15:12Z [Term] @@ -20910,7 +20934,7 @@ intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alp intersection_of: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:19:43Z [Term] @@ -20922,7 +20946,7 @@ is_a: CL:0002395 {is_inferred="true"} ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:27:12Z [Term] @@ -20935,7 +20959,7 @@ is_a: CL:0002395 {is_inferred="true"} ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:30:21Z [Term] @@ -20947,7 +20971,7 @@ is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:38:15Z [Term] @@ -20959,7 +20983,7 @@ is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex relationship: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:47:53Z [Term] @@ -20971,7 +20995,7 @@ is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex relationship: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:47:55Z [Term] @@ -20986,7 +21010,7 @@ intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integ relationship: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:00:52Z [Term] @@ -21001,7 +21025,7 @@ intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integ relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:09:09Z [Term] @@ -21023,7 +21047,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000002980 ! lacks_plasma_membrane_part lymphocyte antigen 6C2 relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:19:25Z [Term] @@ -21038,7 +21062,7 @@ intersection_of: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-pro relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:31:28Z [Term] @@ -21052,7 +21076,7 @@ intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:40:50Z [Term] @@ -21066,7 +21090,7 @@ intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:35:53Z [Term] @@ -21076,10 +21100,11 @@ def: "A goblet cell located in the nasal epithelium." [GOC:cjm, GOC:tfm] subset: cellxgene_subset xref: MP:0002262 is_a: CL:0002370 ! respiratory goblet cell +is_a: CL:0002631 ! epithelial cell of upper respiratory tract intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001826 ! nasal cavity mucosa relationship: part_of UBERON:0005384 ! nasal cavity epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:03:02Z [Term] @@ -21090,7 +21115,7 @@ is_a: CL:0000185 {is_inferred="true"} ! myoepithelial cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:11:48Z [Term] @@ -21101,7 +21126,7 @@ is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:17:05Z [Term] @@ -21112,7 +21137,7 @@ is_a: CL:0002559 ! hair follicle cell is_a: CL:2000000 ! epidermal melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002073 ! hair follicle -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:17:09Z [Term] @@ -21124,7 +21149,7 @@ is_a: CL:0000148 {is_inferred="true"} ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000483 ! epithelium relationship: part_of UBERON:0000483 ! epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:17:14Z [Term] @@ -21137,7 +21162,7 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:25:32Z [Term] @@ -21150,7 +21175,7 @@ is_a: CL:0002491 ! auditory epithelial cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002282 ! stria vascularis of cochlear duct relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:29:15Z [Term] @@ -21158,7 +21183,7 @@ id: CL:0002487 name: cutaneous/subcutaneous mechanoreceptor cell def: "A neuronal receptor that respond to mechanical pressure or distortion in the skin." [GOC:tfm, MP:0000973] is_a: CL:0000199 ! mechanoreceptor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T02:53:30Z [Term] @@ -21173,7 +21198,7 @@ intersection_of: bearer_of PATO:0000586 ! increased size intersection_of: capable_of GO:0001974 ! blood vessel remodeling relationship: bearer_of PATO:0000586 ! increased size relationship: capable_of GO:0001974 ! blood vessel remodeling -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T02:55:24Z [Term] @@ -21190,7 +21215,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:03:38Z [Term] @@ -21201,7 +21226,7 @@ is_a: CL:0002315 ! supporting cell of cochlea intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea relationship: part_of UBERON:0002227 ! spiral organ of cochlea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:09:01Z [Term] @@ -21212,7 +21237,7 @@ is_a: CL:0000098 ! sensory epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:18:43Z [Term] @@ -21220,7 +21245,7 @@ id: CL:0002492 name: strial marginal cell def: "A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria." [GOC:tfm, MP:0004366] is_a: CL:0002491 ! auditory epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:20:41Z [Term] @@ -21230,7 +21255,7 @@ def: "A polarized cell that is juxtaposed to fibrocytes in the underlying spiral comment: Basal cells form a multi-layered epithelial barrier that separates the extracellular spaces of the stria vascularis and the spiral ligament[PMID:18353863] is_a: CL:0002491 ! auditory epithelial cell relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:26:53Z [Term] @@ -21247,7 +21272,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -21258,7 +21283,7 @@ subset: cellxgene_subset synonym: "embryonic cardiomyocyte" EXACT [] synonym: "neonatal cardiomyocyte" EXACT [] is_a: CL:0000746 ! cardiac muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:50:41Z [Term] @@ -21276,7 +21301,7 @@ intersection_of: capable_of GO:0002385 ! mucosal immune response intersection_of: RO:0001025 UBERON:0001277 ! located in intestinal epithelium relationship: capable_of GO:0002385 ! mucosal immune response relationship: RO:0001025 UBERON:0001277 ! located in intestinal epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:54:50Z [Term] @@ -21285,7 +21310,7 @@ name: primary trophoblast giant cell def: "A trophoblast giant cell derived from the mural trophectoderm." [GOC:tfm, PMCID:PMC85124] xref: EMAPA:16066 is_a: CL:0002488 ! trophoblast giant cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T10:07:47Z [Term] @@ -21293,7 +21318,7 @@ id: CL:0002498 name: secondary trophoblast giant cell def: "A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast." [GOC:tfm, PMCID:PMC85124] is_a: CL:0002488 ! trophoblast giant cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T10:07:52Z [Term] @@ -21303,7 +21328,7 @@ def: "A trophoblast cell that arises in the junctional zone (basal plate) of the synonym: "spongiotrophoblast" EXACT [] is_a: CL:0000351 ! trophoblast cell relationship: part_of UBERON:0004021 ! spongiotrophoblast layer -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T12:56:56Z [Term] @@ -21311,7 +21336,7 @@ id: CL:0002500 name: P enteroendocrine cell def: "A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide." [FMA:63418, GOC:tfm] is_a: CL:0002268 ! P/D1 enteroendocrine cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:42:06Z [Term] @@ -21320,7 +21345,7 @@ name: type D1 enteroendocrine cell def: "A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide." [FMA:63207, GOC:tfm] xref: FMA:63207 is_a: CL:0002268 ! P/D1 enteroendocrine cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:42:09Z [Term] @@ -21331,7 +21356,7 @@ synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:63420 is_a: CL:0002272 ! motilin secreting cell is_a: CL:0009006 ! enteroendocrine cell of small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:55:49Z [Term] @@ -21346,7 +21371,7 @@ is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0005742 ! adventitia relationship: part_of UBERON:0005742 ! adventitia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T04:03:56Z [Term] @@ -21359,7 +21384,7 @@ is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-17T03:39:38Z [Term] @@ -21379,7 +21404,7 @@ relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T01:27:41Z [Term] @@ -21399,7 +21424,7 @@ relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T01:27:45Z [Term] @@ -21416,7 +21441,7 @@ relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001293 ! has plasma membrane part C-type lectin domain family 4 member K -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T01:57:00Z [Term] @@ -21435,7 +21460,7 @@ relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alph relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001293 ! lacks_plasma_membrane_part C-type lectin domain family 4 member K relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:13:58Z [Term] @@ -21449,7 +21474,7 @@ intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:07:54Z [Term] @@ -21463,7 +21488,7 @@ intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin a intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:11:14Z [Term] @@ -21475,7 +21500,7 @@ is_a: CL:0002508 {is_inferred="true"} ! langerin-negative, CD103-negative lymph intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:22:15Z [Term] @@ -21487,7 +21512,7 @@ is_a: CL:0002508 {is_inferred="true"} ! langerin-negative, CD103-negative lymph intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:16:21Z [Term] @@ -21496,7 +21521,7 @@ name: Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cel def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "tgd.vg5+.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-24T10:22:18Z [Term] @@ -21505,7 +21530,7 @@ name: Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cel def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "tgd.vg5-.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-24T10:25:44Z [Term] @@ -21516,7 +21541,7 @@ synonym: "interrenal noradrenaline type cell" EXACT [] synonym: "type n interrenal cell" EXACT [] is_a: CL:0000459 ! noradrenergic cell is_a: CL:0002516 ! interrenal chromaffin cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:11:55Z [Term] @@ -21524,7 +21549,7 @@ id: CL:0002516 name: interrenal chromaffin cell def: "A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish." [GOC:MH, GOC:tfm, PMID:12668625] is_a: CL:0000166 ! chromaffin cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:21:35Z [Term] @@ -21535,7 +21560,7 @@ synonym: "interrenal adrenaline secreting cell" RELATED [] synonym: "type a interrenal cell" EXACT [] is_a: CL:0000454 ! epinephrine secreting cell is_a: CL:0002516 ! interrenal chromaffin cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:27:05Z [Term] @@ -21544,12 +21569,12 @@ name: kidney epithelial cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] subset: cellxgene_subset xref: KUPO:0001019 -xref: ZFA:0009374 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009374 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 {is_inferred="true"} ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z [Term] @@ -21557,7 +21582,7 @@ id: CL:0002519 name: interrenal epithelial cell def: "An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type." [GOC:mh, GOC:tfm, PMID:12668625] is_a: CL:0002518 ! kidney epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T11:03:32Z [Term] @@ -21568,7 +21593,7 @@ xref: BTO:0004597 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002522 ! renal filtration cell relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:34:56Z [Term] @@ -21582,8 +21607,8 @@ is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0002190 ! subcutaneous adipose tissue relationship: part_of UBERON:0002190 ! subcutaneous adipose tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-21T02:51:22Z [Term] @@ -21592,19 +21617,19 @@ name: renal filtration cell def: "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." [GOC:tfm] is_a: CL:0000424 ! excretory cell relationship: part_of UBERON:0001008 ! renal system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:37:59Z [Term] id: CL:0002523 name: mesonephric podocyte -def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros." [GOC:tfm] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-2244-7917"} +def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros." [GOC:tfm] {terms:contributor="https://orcid.org/0000-0002-2244-7917"} synonym: "mesonephric glomerular visceral epithelial cell" EXACT [ZFA:0001674] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:58:30Z [Term] @@ -21612,7 +21637,7 @@ id: CL:0002524 name: disseminated nephrocyte def: "A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues." [GOC:tfm, PMID:19783135] is_a: CL:0002520 ! nephrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T02:07:33Z [Term] @@ -21624,7 +21649,7 @@ is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0000081 ! metanephros -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T02:02:13Z [Term] @@ -21758,7 +21783,7 @@ is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000002 ! uterine cervix relationship: part_of UBERON:0004801 ! cervix epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-24T08:20:08Z [Term] @@ -21771,8 +21796,8 @@ is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000305 ! amnion relationship: part_of UBERON:0000305 ! amnion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T12:38:01Z [Term] @@ -21784,7 +21809,7 @@ is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0000305 ! amnion relationship: part_of UBERON:0000305 ! amnion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T12:44:24Z [Term] @@ -21793,12 +21818,12 @@ name: intrahepatic cholangiocyte def: "An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes." [GOC:tfm, PMID:23720296] subset: cellxgene_subset synonym: "small bile duct cholangiocyte" EXACT [PMID:23720296] -xref: ZFA:0009379 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009379 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000488 {is_inferred="true"} ! cholangiocyte intersection_of: CL:1000488 ! cholangiocyte intersection_of: part_of UBERON:0004823 ! intrahepatic bile duct epithelium relationship: part_of UBERON:0004823 ! intrahepatic bile duct epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T01:20:20Z [Term] @@ -21811,7 +21836,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0004178 ! aorta smooth muscle tissue relationship: part_of UBERON:0004178 ! aorta smooth muscle tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T01:42:12Z [Term] @@ -21822,7 +21847,7 @@ is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T01:47:47Z [Term] @@ -21833,7 +21858,7 @@ is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0003124 ! chorion membrane relationship: part_of UBERON:0003124 ! chorion membrane -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T03:04:35Z [Term] @@ -21851,8 +21876,8 @@ is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T03:48:11Z [Term] @@ -21863,7 +21888,7 @@ subset: cellxgene_subset xref: BTO:0003245 xref: CALOHA:TS-0047 is_a: CL:1000413 ! endothelial cell of artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T03:54:42Z [Term] @@ -21874,7 +21899,7 @@ is_a: CL:0002544 {is_inferred="true"} ! aortic endothelial cell intersection_of: CL:0002544 ! aortic endothelial cell intersection_of: part_of UBERON:0001515 ! thoracic aorta relationship: part_of UBERON:0001515 ! thoracic aorta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T03:59:09Z [Term] @@ -21882,9 +21907,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -21895,7 +21920,7 @@ is_a: CL:1000306 {is_inferred="true"} ! fibroblast of tunica adventitia of arter intersection_of: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia relationship: part_of UBERON:0004664 ! aorta tunica adventitia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:43:41Z [Term] @@ -21909,7 +21934,7 @@ is_a: CL:0002494 {is_inferred="true"} ! cardiocyte intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:57:44Z [Term] @@ -21921,7 +21946,7 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: part_of UBERON:0001886 ! choroid plexus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:01:39Z [Term] @@ -21932,7 +21957,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001811 ! conjunctiva relationship: part_of UBERON:0001811 ! conjunctiva -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:03:44Z [Term] @@ -21943,7 +21968,7 @@ is_a: CL:0002620 {is_inferred="true"} ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:05:33Z [Term] @@ -21954,7 +21979,7 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001828 ! gingiva relationship: part_of UBERON:0001828 ! gingiva -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:09:12Z [Term] @@ -21968,7 +21993,7 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:11:03Z [Term] @@ -21979,7 +22004,7 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001473 ! lymphatic vessel relationship: part_of UBERON:0001473 ! lymphatic vessel -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:16:18Z [Term] @@ -21991,7 +22016,7 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:18:38Z [Term] @@ -22002,7 +22027,7 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001758 ! periodontium relationship: part_of UBERON:0001758 ! periodontium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:19:48Z [Term] @@ -22014,8 +22039,8 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:22:27Z [Term] @@ -22025,8 +22050,8 @@ def: "A fibroblast that is part of villous mesenchyme." [GOC:tfm] subset: human_reference_atlas is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:24:28Z [Term] @@ -22037,7 +22062,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002073 ! hair follicle relationship: part_of UBERON:0002073 ! hair follicle -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:11:01Z [Term] @@ -22049,7 +22074,7 @@ is_a: CL:0002559 {is_inferred="true"} ! hair follicle cell intersection_of: CL:0002559 ! hair follicle cell intersection_of: part_of UBERON:0005941 ! hair inner root sheath relationship: part_of UBERON:0005941 ! hair inner root sheath -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:27:51Z [Term] @@ -22061,7 +22086,7 @@ is_a: CL:0002559 {is_inferred="true"} ! hair follicle cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005942 ! hair outer root sheath relationship: part_of UBERON:0005942 ! hair outer root sheath -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:29:47Z [Term] @@ -22074,7 +22099,7 @@ is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000362 ! epidermal cell intersection_of: part_of UBERON:0006004 ! hair follicle matrix region relationship: part_of UBERON:0006004 ! hair follicle matrix region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:31:06Z [Term] @@ -22082,12 +22107,12 @@ id: CL:0002563 name: intestinal epithelial cell def: "An epithelial cell of the intestine." [GOC:tfm] subset: cellxgene_subset -xref: ZFA:0009399 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009399 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001277 ! intestinal epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:18:31Z [Term] @@ -22098,7 +22123,7 @@ is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002242 ! nucleus pulposus relationship: part_of UBERON:0002242 ! nucleus pulposus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T02:12:23Z [Term] @@ -22112,8 +22137,8 @@ is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium relationship: part_of UBERON:0002506 ! iris epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:28:52Z [Term] @@ -22123,7 +22148,7 @@ def: "A melanocyte that appears darker due to content or amount of melanin granu synonym: "melanotic melanocyte" EXACT [PMID:10985850] synonym: "melanotic melanophore" EXACT [PMID:10985850] is_a: CL:0000148 ! melanocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:57:11Z [Term] @@ -22133,7 +22158,7 @@ def: "A melanocyte that appears lighter in color." [GOC:tfm] synonym: "amelanotic melanocyte" EXACT [PMID:10985850] synonym: "amelanotic melanophore" EXACT [PMID:10985850] is_a: CL:0000148 ! melanocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:58:23Z [Term] @@ -22142,8 +22167,8 @@ name: mesenchymal stem cell of Wharton's jelly def: "A mesenchymal stem cell that is part of Wharton's jelly." [GOC:tfm] subset: human_reference_atlas is_a: CL:0002569 ! mesenchymal stem cell of umbilical cord -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:51:18Z [Term] @@ -22155,7 +22180,7 @@ is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0003422 ! mesenchyme of umbilical cord relationship: part_of UBERON:0003422 ! mesenchyme of umbilical cord -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:55:12Z [Term] @@ -22168,7 +22193,7 @@ is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: part_of UBERON:0001013 ! adipose tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:57:17Z [Term] @@ -22179,7 +22204,7 @@ is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0002195 ! hepatic stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:58:51Z [Term] @@ -22191,7 +22216,7 @@ is_a: CL:0001035 ! bone cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002412 ! vertebra relationship: part_of UBERON:0002412 ! vertebra -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T10:40:27Z [Term] @@ -22206,8 +22231,8 @@ xref: CALOHA:TS-0898 xref: MESH:D012583 is_a: CL:0000125 ! glial cell relationship: part_of UBERON:0000010 ! peripheral nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T01:19:27Z [Term] @@ -22219,8 +22244,8 @@ is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T02:40:41Z [Term] @@ -22232,7 +22257,7 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T02:54:18Z [Term] @@ -22245,8 +22270,8 @@ synonym: "perineurial glial cell" EXACT [PMID:25818566] is_a: CL:0000125 ! glial cell is_a: CL:0002320 ! connective tissue cell relationship: part_of UBERON:0000121 ! perineurium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T03:03:58Z [Term] @@ -22258,7 +22283,7 @@ is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T03:21:30Z [Term] @@ -22269,7 +22294,7 @@ is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002095 ! mesentery relationship: part_of UBERON:0002095 ! mesentery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:19:40Z [Term] @@ -22280,7 +22305,7 @@ is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0003688 ! omentum relationship: part_of UBERON:0003688 ! omentum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:19:42Z [Term] @@ -22291,7 +22316,7 @@ is_a: CL:0002334 {is_inferred="true"} ! preadipocyte is_a: CL:4006000 ! fibroblast of breast intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0000310 ! breast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:19:46Z [Term] @@ -22302,7 +22327,7 @@ is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0005406 ! perirenal fat relationship: part_of UBERON:0005406 ! perirenal fat -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:20:04Z [Term] @@ -22310,7 +22335,7 @@ id: CL:0002582 name: visceral preadipocyte def: "A preadipocyte that is part of visceral tissue." [GOC:tfm] is_a: CL:0002334 ! preadipocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:32:56Z [Term] @@ -22321,7 +22346,7 @@ is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002072 ! hypodermis relationship: part_of UBERON:0002072 ! hypodermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:33:01Z [Term] @@ -22346,8 +22371,8 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T03:28:27Z [Term] @@ -22366,8 +22391,8 @@ intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T03:37:09Z [Term] @@ -22378,7 +22403,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002066 ! umbilical vein relationship: part_of UBERON:0002066 ! umbilical vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:00:51Z [Term] @@ -22389,7 +22414,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001529 ! brachiocephalic artery relationship: part_of UBERON:0001529 ! brachiocephalic artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:00:58Z [Term] @@ -22401,7 +22426,7 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:20Z [Term] @@ -22415,8 +22440,8 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0002012 ! pulmonary artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:28Z [Term] @@ -22429,8 +22454,8 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001621 ! coronary artery relationship: part_of UBERON:0001621 ! coronary artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:34Z [Term] @@ -22441,7 +22466,7 @@ is_a: CL:0002595 ! smooth muscle cell of the subclavian artery intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002456 ! internal thoracic artery relationship: part_of UBERON:0002456 ! internal thoracic artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:41Z [Term] @@ -22452,7 +22477,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001310 ! umbilical artery relationship: part_of UBERON:0001310 ! umbilical artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:48Z [Term] @@ -22463,7 +22488,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001533 ! subclavian artery relationship: part_of UBERON:0001533 ! subclavian artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:52Z [Term] @@ -22474,7 +22499,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0005396 ! carotid artery segment relationship: part_of UBERON:0005396 ! carotid artery segment -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:56Z [Term] @@ -22487,8 +22512,8 @@ is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:1001319 ! bladder cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001255 ! urinary bladder -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:43:24Z [Term] @@ -22502,8 +22527,8 @@ is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:46:39Z [Term] @@ -22514,7 +22539,7 @@ is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:48:17Z [Term] @@ -22526,7 +22551,7 @@ is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:50:28Z [Term] @@ -22538,7 +22563,7 @@ is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:53:28Z [Term] @@ -22550,7 +22575,7 @@ is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0004715 ! annulus fibrosus disci intervertebralis relationship: part_of UBERON:0004715 ! annulus fibrosus disci intervertebralis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T06:50:53Z [Term] @@ -22563,7 +22588,7 @@ is_a: CL:2000005 ! brain macroglial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002037 ! cerebellum relationship: part_of UBERON:0002037 ! cerebellum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T06:57:27Z [Term] @@ -22577,8 +22602,8 @@ is_a: CL:0002605 ! astrocyte of the cerebral cortex is_a: CL:1001580 ! hippocampal glial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002421 ! hippocampal formation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T06:57:33Z [Term] @@ -22591,8 +22616,8 @@ is_a: CL:0012000 ! astrocyte of the forebrain is_a: CL:1001579 ! cerebral cortex glial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000956 ! cerebral cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T06:57:36Z [Term] @@ -22603,7 +22628,7 @@ is_a: CL:0000127 {is_inferred="true"} ! astrocyte intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:11:26Z [Term] @@ -22612,7 +22637,7 @@ name: migratory enteric neural crest cell def: "A neural crest cell that gives rise to cells of the enteric nervous system." [GOC:tfm] subset: cellxgene_subset is_a: CL:0000333 ! migratory neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:24:35Z [Term] @@ -22624,7 +22649,7 @@ is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002421 ! has soma location hippocampal formation relationship: RO:0002100 UBERON:0002421 ! has soma location hippocampal formation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:31:49Z [Term] @@ -22636,7 +22661,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0004684 ! has soma location raphe nuclei relationship: RO:0002100 UBERON:0004684 ! has soma location raphe nuclei -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:42:06Z [Term] @@ -22648,7 +22673,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord relationship: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:43:34Z [Term] @@ -22660,7 +22685,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord relationship: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:46:03Z [Term] @@ -22671,7 +22696,7 @@ is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002435 ! has soma location striatum relationship: RO:0002100 UBERON:0002435 ! has soma location striatum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:47:12Z [Term] @@ -22683,7 +22708,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002038 ! has soma location substantia nigra relationship: RO:0002100 UBERON:0002038 ! has soma location substantia nigra -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:48:42Z [Term] @@ -22696,7 +22721,7 @@ is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0003688 ! omentum relationship: part_of UBERON:0003688 ! omentum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T10:17:00Z [Term] @@ -22709,7 +22734,7 @@ is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0005406 ! perirenal fat relationship: part_of UBERON:0005406 ! perirenal fat -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T10:17:05Z [Term] @@ -22725,7 +22750,7 @@ is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0000310 ! breast relationship: part_of UBERON:0000310 ! breast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T10:17:07Z [Term] @@ -22737,7 +22762,7 @@ is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002066 ! umbilical vein relationship: part_of UBERON:0002066 ! umbilical vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T11:36:51Z [Term] @@ -22748,10 +22773,10 @@ comment: The existence of adult endothelial progenitor cells has been controvers subset: human_reference_atlas synonym: "EPC" EXACT [] is_a: CL:0000566 ! angioblastic mesenchymal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1410" xsd:string property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/348" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T12:11:18Z [Term] @@ -22766,8 +22791,8 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T12:31:49Z [Term] @@ -22778,7 +22803,7 @@ is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001949 ! gingival epithelium relationship: part_of UBERON:0001949 ! gingival epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T12:46:28Z [Term] @@ -22791,7 +22816,7 @@ is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T02:11:10Z [Term] @@ -22803,7 +22828,7 @@ is_a: CL:0000622 {is_inferred="true"} ! acinar cell is_a: CL:1001596 ! salivary gland glandular cell intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0001044 ! saliva-secreting gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T02:22:22Z [Term] @@ -22814,7 +22839,7 @@ is_a: CL:0000510 {is_inferred="true"} ! paneth cell is_a: CL:1001585 ! appendix glandular cell intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-15T09:38:18Z [Term] @@ -22826,7 +22851,7 @@ is_a: CL:0000077 {is_inferred="true"} ! mesothelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis relationship: part_of UBERON:0004813 ! seminiferous tubule epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-15T11:59:23Z [Term] @@ -22881,30 +22906,30 @@ id: CL:0002630 name: actinomycete-type spore def: "A spore formed from bacteria in the order Actinomycetales." [GO:0034304, GOC:tfm] is_a: CL:0000520 ! prokaryotic cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-16T01:01:41Z [Term] id: CL:0002631 name: epithelial cell of upper respiratory tract -def: "Any respiratory epithelial cell that is part of some upper respiratory tract." [FBC:Autogenerated] -is_a: CL:0002368 {is_inferred="true"} ! respiratory epithelial cell -intersection_of: CL:0002368 ! respiratory epithelial cell -intersection_of: part_of UBERON:0001557 ! upper respiratory tract -relationship: part_of UBERON:0001557 ! upper respiratory tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +def: "Any epithelial cell that is part of some upper respiratory tract epithelium." [FBC:Autogenerated] +is_a: CL:0002368 ! respiratory epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0004814 ! upper respiratory tract epithelium +relationship: part_of UBERON:0004814 ! upper respiratory tract epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T12:28:55Z [Term] id: CL:0002632 name: epithelial cell of lower respiratory tract -def: "Any respiratory epithelial cell that is part of some lower respiratory tract." [FBC:Autogenerated] +def: "Any epithelial cell that is part of some lower respiratory tract epithelium." [FBC:Autogenerated] subset: cellxgene_subset -is_a: CL:0002368 {is_inferred="true"} ! respiratory epithelial cell -intersection_of: CL:0002368 ! respiratory epithelial cell -intersection_of: part_of UBERON:0001558 ! lower respiratory tract -relationship: part_of UBERON:0001558 ! lower respiratory tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +is_a: CL:0002368 ! respiratory epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0004815 ! lower respiratory tract epithelium +relationship: part_of UBERON:0004815 ! lower respiratory tract epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T12:29:31Z [Term] @@ -22915,8 +22940,10 @@ subset: cellxgene_subset synonym: "airway basal cell" EXACT [] synonym: "airway basal stem cell" EXACT [] is_a: CL:0000646 ! basal cell -is_a: CL:0002368 ! respiratory epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: CL:0000646 ! basal cell +intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium +relationship: part_of UBERON:0004802 ! respiratory tract epithelium +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T03:11:10Z [Term] @@ -22927,7 +22954,7 @@ is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0009882 ! anal column relationship: part_of UBERON:0009882 ! anal column -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T12:11:38Z [Term] @@ -22936,7 +22963,7 @@ name: nonkeratinized epithelial cell of anal column def: "A nonkeratinized epithelial cell of the anal canal." [GOC:tfm] xref: FMA:263146 is_a: CL:0002634 ! epithelial cell of anal column -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:05:33Z [Term] @@ -22946,7 +22973,7 @@ def: "A nonkeratinized cell epithleial cell of the inferior part of the anal can xref: FMA:263144 is_a: CL:0002635 ! nonkeratinized epithelial cell of anal column is_a: CL:1000438 ! epithelial cell of wall of inferior part of anal canal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:06:53Z [Term] @@ -22958,7 +22985,7 @@ is_a: CL:0002634 ! epithelial cell of anal column is_a: CL:0009066 ! stratified squamous epithelial cell of anal canal intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: part_of UBERON:0000159 ! anal canal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:08:40Z [Term] @@ -22967,13 +22994,11 @@ name: bronchioalveolar stem cell def: "A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc." [GOC:tfm, MP:0011691, PMID:15960971] synonym: "basal epithelial cell of bronchioalveolar duct junction" EXACT [] synonym: "BASC" EXACT [] -is_a: CL:1000350 ! basal cell of epithelium of terminal bronchiole -is_a: CL:1000351 ! basal cell of epithelium of respiratory bronchiole -intersection_of: CL:0002633 ! respiratory basal cell -intersection_of: part_of UBERON:0001955 ! epithelium of respiratory bronchiole -intersection_of: part_of UBERON:0001958 ! terminal bronchiole epithelium -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell +relationship: part_of UBERON:0002051 ! epithelium of bronchiole +relationship: part_of UBERON:0004903 ! bronchoalveolar duct junction +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T03:26:08Z [Term] @@ -22983,7 +23008,7 @@ def: "An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fl comment: Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002323 ! amniocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T03:55:39Z [Term] @@ -22991,7 +23016,7 @@ id: CL:0002640 name: amniotic epithelial stem cell def: "An epithelial fate stem cell derived form the amnion membrane." [GOC:tfm, PMID:20446274] is_a: CL:0000036 ! epithelial fate stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T04:06:17Z [Term] @@ -23000,7 +23025,7 @@ name: epithelial cell of esophageal gland proper def: "An epithelial cell of the esophageal gland proper." [GOC:tfm] xref: FMA:256141 is_a: CL:0002657 ! glandular cell of esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:16:51Z [Term] @@ -23009,7 +23034,7 @@ name: epithelial cell of esophageal cardiac gland def: "An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia." [GOC:tfm, http://web.mac.com/wjkrause/iWeb/Histology/Blog/E3FA5916-1AA9-4885-B579-5051838D98CB.html] xref: FMA:256143 is_a: CL:0002657 ! glandular cell of esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:16:54Z [Term] @@ -23018,7 +23043,7 @@ name: nonkeratinized cell of stratum corneum of esophageal epithelium def: "An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin." [GOC:tfm] xref: FMA:263148 is_a: CL:0002654 ! epithelial cell of stratum corneum of esophageal epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:22:09Z [Term] @@ -23027,7 +23052,7 @@ name: endo-epithelial cell of tympanic part of viscerocranial mucosa def: "An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70628 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:25:44Z [Term] @@ -23036,7 +23061,7 @@ name: endo-epithelial cell of pharyngotympanic part of viscerocranial mucosa def: "An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa." [GOC:tfm] xref: FMA:70629 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:25:46Z [Term] @@ -23044,7 +23069,7 @@ id: CL:0002646 name: obsolete epithelial cell of buccal part of viscerocranial mucosa def: "An ecto-epithelial cell of the buccal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70577 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:34:12Z @@ -23053,7 +23078,7 @@ id: CL:0002647 name: obsolete epithelial cell of anterior palatal part of viscerocranial mucosa def: "An ecto-epithelial cell of the palatal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70580 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:34:14Z @@ -23062,7 +23087,7 @@ id: CL:0002648 name: obsolete epithelial cell of nasal part of viscerocranial mucosa def: "An ecto-epithelial cell of the nasal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70554 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:36:06Z @@ -23071,7 +23096,7 @@ id: CL:0002649 name: obsolete epithelial cell of gingival part of viscerocranial mucosa def: "An ecto-epithelial cell of the gingival region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70579 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:36:11Z @@ -23080,7 +23105,7 @@ id: CL:0002650 name: obsolete epithelial cell of paranasal sinus part of viscerocranial mucosa def: "An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70578 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:38:18Z @@ -23091,7 +23116,7 @@ def: "An endothelial cell that is part of the venous sinus of spleen. This endot synonym: "stave cell" EXACT [FMA:62817] xref: FMA:72140 is_a: CL:0002262 ! endothelial cell of sinusoid -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:06:49Z [Term] @@ -23103,22 +23128,20 @@ subset: human_reference_atlas synonym: "endothelial cell of postcapillary venule of lymph node" BROAD [] synonym: "HEV cell" EXACT [] xref: FMA:67759 -is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:1000414 ! endothelial cell of venule -intersection_of: CL:0000115 ! endothelial cell +intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:8410037 ! high endothelial venule relationship: part_of UBERON:8410037 ! high endothelial venule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:14:10Z [Term] id: CL:0002653 name: squamous endothelial cell -def: "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [GOC:tfm] -is_a: CL:0000076 ! squamous epithelial cell -is_a: CL:1000414 ! endothelial cell of venule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +def: "A squamous shaped endothelial cell." [GOC:dos] +is_a: CL:0000115 ! endothelial cell +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:31:25Z [Term] @@ -23127,7 +23150,7 @@ name: epithelial cell of stratum corneum of esophageal epithelium def: "An epithelial cell of stratum corneum of esophageal epithelium." [GOC:tfm] xref: FMA:70733 is_a: CL:0002252 ! epithelial cell of esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:46:35Z [Term] @@ -23136,7 +23159,7 @@ name: epithelial cell of stratum spinosum of esophageal epithelium def: "An epithelial cell of stratum spinosum of esophageal epithelium." [GOC:tfm] xref: FMA:70732 is_a: CL:0002252 ! epithelial cell of esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:48:26Z [Term] @@ -23148,7 +23171,7 @@ is_a: CL:1001591 ! oviduct glandular cell intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0001295 ! endometrium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:54:08Z [Term] @@ -23161,7 +23184,7 @@ is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0002252 {is_inferred="true"} ! epithelial cell of esophagus intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0001043 ! esophagus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:55:57Z [Term] @@ -23173,7 +23196,7 @@ is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T04:03:01Z [Term] @@ -23186,7 +23209,7 @@ is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0002178 ! epithelial cell of stomach intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000945 ! stomach -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:20:35Z [Term] @@ -23196,7 +23219,7 @@ def: "A luminal epithelial cell of mammary gland located in acinus of structure. comment: Consider if synonymous with mammary alveolar cell CL:0002325. Some use this term to refer to the non-lactating cell type that gives rise to the lactating cell type. xref: FMA:74505 is_a: CL:0002326 ! luminal epithelial cell of mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:44:31Z [Term] @@ -23205,7 +23228,7 @@ name: luminal cell of lactiferous terminal ductal lobular unit def: "A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into." [GOC:tfm] xref: FMA:87168 is_a: CL:0002662 ! luminal cell of lactiferous duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:44:33Z [Term] @@ -23214,7 +23237,7 @@ name: luminal cell of lactiferous duct def: "A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive." [GOC:tfm, PMID:19022771] xref: FMA:74504 is_a: CL:0002326 ! luminal epithelial cell of mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:44:48Z [Term] @@ -23226,7 +23249,7 @@ is_a: CL:0002074 {is_inferred="true"} ! myocardial endocrine cell intersection_of: CL:0002074 ! myocardial endocrine cell intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T02:45:39Z [Term] @@ -23237,7 +23260,7 @@ comment: Discrepancy in develops from origins prevents me from making the assert synonym: "cardiovascular progenitor cell" EXACT [PMID:17519333, PMID:19745164] synonym: "CPC" RELATED OMO:0003000 [PMID:19745164] is_a: CL:0000048 ! multi fate stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:15:38Z [Term] @@ -23246,7 +23269,7 @@ name: otic fibrocyte def: "A fibrocyte of the cochlea that has specialized structural and molecular adaptions." [GOC:tfm, PMID:18353863] is_a: CL:0000135 ! fibrocyte relationship: part_of UBERON:0006725 ! spiral ligament -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:35:01Z [Term] @@ -23256,7 +23279,7 @@ def: "An otic fibrocyte that underlies the spiral prominence and is part of a me synonym: "type II otic fibrocyte" EXACT [] synonym: "type II spiral ligament fibrocyte" EXACT [MP:0004488] is_a: CL:0002665 ! otic fibrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:40Z [Term] @@ -23266,7 +23289,7 @@ def: "An otic fibrocyte that resides above the stria vasularis and is part of a synonym: "type V otic fibrocyte" EXACT [] synonym: "type V spiral ligament fibrocyte" EXACT [] is_a: CL:0002665 ! otic fibrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:42Z [Term] @@ -23276,7 +23299,7 @@ def: "An otic fibrocyte that is lateral to the basilar membrane and anchoris it synonym: "type IV otic fibrocyte" EXACT [] synonym: "type IV spiral ligament fibrocyte" EXACT [MP:0004490] is_a: CL:0002665 ! otic fibrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:46Z [Term] @@ -23286,7 +23309,7 @@ def: "An otic fibrocyte that lines the otic capsule." [GOC:tfm, PMID:18353863] synonym: "type III otic fibrocyte" EXACT [] synonym: "type III spiral ligament fibrocyte" EXACT [MP:0004489] is_a: CL:0002665 ! otic fibrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:50Z [Term] @@ -23296,7 +23319,7 @@ def: "An otic fibrocyte that underlies the stria vascularis and is part of a mes synonym: "type I otic fibrocyte" EXACT [] synonym: "type I spiral ligament fibrocyte" EXACT [MP:0004487] is_a: CL:0002665 ! otic fibrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:39:27Z [Term] @@ -23305,7 +23328,7 @@ name: endothelial stalk cell def: "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." [GOC:tfm, PMID:21521739] subset: cellxgene_subset is_a: CL:0000071 ! blood vessel endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T01:49:32Z [Term] @@ -23315,7 +23338,7 @@ def: "A multi-fate stem cell that can give rise to different retinal cell types is_a: BFO:0000002 is_a: CL:0000048 ! multi fate stem cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T02:38:01Z [Term] @@ -23327,7 +23350,7 @@ is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: part_of UBERON:0000378 ! tongue muscle relationship: part_of UBERON:0000378 ! tongue muscle -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T03:10:02Z [Term] @@ -23337,7 +23360,7 @@ def: "A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 l synonym: "H- cell" EXACT [] is_a: CL:0000521 ! fungal cell relationship: RO:0002162 NCBITaxon:4896 ! in taxon Schizosaccharomyces pombe -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T03:20:53Z [Term] @@ -23346,7 +23369,7 @@ name: H plus def: "A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus." [GOC:tfm] is_a: CL:0000521 ! fungal cell relationship: RO:0002162 NCBITaxon:4896 ! in taxon Schizosaccharomyces pombe -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T03:20:58Z [Term] @@ -23356,7 +23379,7 @@ def: "A neuroblast derived from a neural crest cell." [GOC:tfm, PMID:17407019] is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-22T09:24:15Z [Term] @@ -23371,8 +23394,8 @@ synonym: "naive regulatory T-cell" EXACT [] synonym: "naive regulatory T-lymphocyte" EXACT [] is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000898 ! naive T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-25T03:17:21Z [Term] @@ -23385,7 +23408,7 @@ is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: output_of GO:0043379 ! memory T cell differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-25T03:17:34Z [Term] @@ -23415,7 +23438,7 @@ relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like pr relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-29T10:08:02Z [Term] @@ -23426,7 +23449,7 @@ is_a: CL:0000696 {is_inferred="true"} ! PP cell is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000696 ! PP cell intersection_of: part_of UBERON:0000160 ! intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-09-27T11:59:01Z [Term] @@ -23437,7 +23460,7 @@ is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001225 ! cortex of kidney -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0956-8634 +property_value: terms:contributor https://orcid.org/0000-0002-0956-8634 creation_date: 2011-10-25T03:49:41Z [Term] @@ -23450,8 +23473,8 @@ is_a: CL:0000740 ! retinal ganglion cell is_a: CL:0004247 ! bistratified cell intersection_of: CL:0000740 ! retinal ganglion cell intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003002 @@ -23460,8 +23483,8 @@ namespace: cell def: "A retinal ganglion cell that has a small dendritic field and a medium dendritic arbor with post sympatic terminals in sublaminar layer S3." [PMID:11978858] is_a: CL:0000740 ! retinal ganglion cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003003 @@ -23471,8 +23494,8 @@ def: "A mono-stratified retinal ganglion cell that has a small dendritic field a is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003004 @@ -23484,8 +23507,8 @@ is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 relationship: RO:0013001 UBERON:0009851 ! has synaptic IO in region border of sublaminar layers S4 and S5 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003005 @@ -23495,8 +23518,8 @@ def: "A mono-stratified retinal ganglion cell that has a small dendritic field a comment: Masland nomenclature PMID:11978858 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003006 @@ -23507,8 +23530,8 @@ is_a: CL:0003005 ! G4 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003007 @@ -23520,8 +23543,8 @@ is_a: CL:0003005 ! G4 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003008 @@ -23531,8 +23554,8 @@ def: "A mono-stratified retinal ganglion cell that has a medium dendritic field is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003009 @@ -23543,8 +23566,8 @@ is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003010 @@ -23555,8 +23578,8 @@ synonym: "ON-OFF DS" EXACT [] is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003011 @@ -23566,8 +23589,8 @@ def: "A mono-stratified retinal ganglion cell that has a large dendritic field a is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003012 @@ -23578,8 +23601,8 @@ is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003013 @@ -23633,8 +23656,8 @@ namespace: cell def: "A retinal ganglion B cell that has post synaptic terminals in S2." [PMID:12209831] is_a: CL:0004183 ! retinal ganglion cell B3 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003018 @@ -23644,8 +23667,8 @@ def: "A retinal ganglion B3 cell with dentrites terminating in S4." [PMID:122098 xref: BAMS:1010 is_a: CL:0004183 ! retinal ganglion cell B3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003020 @@ -23654,8 +23677,8 @@ namespace: cell def: "A retinal ganglion cell C that has post-synaptic terminals in S2." [PMID:12209831] is_a: CL:0004116 ! retinal ganglion cell C relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003021 @@ -23663,8 +23686,8 @@ name: retinal ganglion cell C4 namespace: cell def: "A retinal ganglion cell C outer that has a medium dendritic field and a dense dendritic arbor." [PMID:12209831] is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003022 @@ -23672,8 +23695,8 @@ name: retinal ganglion cell C5 namespace: cell def: "A retinal ganglion cell C outer that has medium dendritic density and field size." [PMID:12209831] is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003023 @@ -23681,8 +23704,8 @@ name: retinal ganglion cell C6 namespace: cell def: "A retinal ganglion cell C outer that has dense dendritic diversity." [PMID:12209831] is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003024 @@ -23691,8 +23714,8 @@ namespace: cell def: "A retinal ganglion cell C with medium cell bodies and large dendritic field." [PMID:12209831] is_a: CL:0004116 ! retinal ganglion cell C relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003025 @@ -23701,8 +23724,8 @@ namespace: cell def: "A retinal ganglion cell C inner that has sparse dendritic density, and large dendritic field." [PMID:12209831] synonym: "epsilon" RELATED [] is_a: CL:0003024 ! retinal ganglion cell C inner -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003026 @@ -23712,8 +23735,8 @@ def: "A bistratified retinal ganglion cell that has a small dendrite fields with is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003027 @@ -23725,8 +23748,8 @@ synonym: "ON-OFF direction selective" RELATED [] is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003028 @@ -23736,8 +23759,8 @@ def: "A monostratified retinal ganglion cell that has a small dendrite field wit is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003029 @@ -23748,8 +23771,8 @@ is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003030 @@ -23758,8 +23781,8 @@ namespace: cell def: "A monostratified retinal ganglion cell that has a medium soma and a small dendrite field." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003031 @@ -23769,8 +23792,8 @@ def: "A monostratified retinal ganglion cell that has post synaptic terminals in is_a: CL:0003030 ! M3 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003032 @@ -23780,8 +23803,8 @@ def: "A monostratified retinal ganglion cell that has post synaptic terminals in is_a: CL:0003030 ! M3 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003033 @@ -23791,8 +23814,8 @@ def: "A monostratified retinal ganglion cell that has a large soma, a medium den is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003034 @@ -23802,8 +23825,8 @@ def: "A monostratified retinal ganglion cell that has a small soma, an assymetri is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003035 @@ -23813,8 +23836,8 @@ def: "A monostratified retinal ganglion cell that contains opsin." [PMID:1662686 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0002292 PR:000001243 ! expresses melanopsin -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003036 @@ -23823,8 +23846,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 2 and 5." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003037 @@ -23834,8 +23857,8 @@ def: "An M7 retinal ganglion cells with synaptic terminals in S4 and is depolari is_a: CL:0003036 ! M7 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003038 @@ -23845,8 +23868,8 @@ def: "An M7 retinal ganglion cells with synaptic terminals in S2 and is depolari is_a: CL:0003036 ! M7 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003039 @@ -23855,8 +23878,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and medium dendritic field, with dense dendritic arbor." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003040 @@ -23865,8 +23888,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 1 and 5." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003041 @@ -23876,8 +23899,8 @@ def: "An M9 retinal ganglion cells with synaptic terminals in S2 and is depolari is_a: CL:0003040 ! M9 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003042 @@ -23887,8 +23910,8 @@ def: "An M9 retinal ganglion cell with synaptic terminals in S4 that is depolari is_a: CL:0003040 ! M9 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003043 @@ -23897,8 +23920,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with dense dendritic arbor." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003044 @@ -23908,8 +23931,8 @@ def: "A bistratified ganglion cell with small, dense dendritic fields that termi is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003045 @@ -23919,8 +23942,8 @@ def: "A bistratified ganglion cell with larger, asymetric dendritic fields that is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003046 @@ -23930,8 +23953,8 @@ def: "A bistratifed retinal ganglion cell that has small, symmetric dendritic fi is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003047 @@ -23941,8 +23964,8 @@ def: "A bistratifed retinal ganglion cell that has small, symmetric dendritic fi is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008929 ! has synaptic IO in region sublaminar layers S4 or S5 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003048 @@ -23956,7 +23979,7 @@ synonym: "long- (L) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/eL synonym: "long-wavelength cone" EXACT [https://doi.org/10.1038/323623a0] is_a: CL:0000573 ! retinal cone cell relationship: has_part PR:000001244 ! long-wave-sensitive opsin 1 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003049 @@ -23970,7 +23993,7 @@ synonym: "middle- (M) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/ synonym: "middle-wavelength-sensitive (M) cone" EXACT [https://opg.optica.org/josaa/abstract.cfm?URI=josaa-6-1-153] is_a: CL:0000573 ! retinal cone cell relationship: has_part PR:000001224 ! medium-wave-sensitive opsin -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003050 @@ -23987,7 +24010,7 @@ synonym: "short- (S) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/e synonym: "short-wavelength sensitive cone" EXACT [PMID:31117170] synonym: "short-wavelength-sensitive (S) cone" EXACT [https://opg.optica.org/josaa/abstract.cfm?URI=josaa-6-1-153] is_a: CL:0000573 ! retinal cone cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003051 @@ -23995,7 +24018,7 @@ name: UV cone cell namespace: cell def: "A cone cell that detects ultraviolet (UV) wavelength light." [] is_a: CL:0000573 ! retinal cone cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004001 @@ -24014,8 +24037,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with small to medium soma and small to medium dendritic field." [PMID:12209831] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004116 @@ -24024,8 +24047,8 @@ namespace: cell def: "A retinal ganglion with cell medium cell bodies and medium to large dendritic fields." [PMID:12209831] comment: Group RGC cells are defined as having small to medium cell bodies and medium to large dendritic fields. Their morphology was more heterogeneous than that of Groups RGA and RGB. We classified cells with a large soma and a large dendritic field as RGA, cells with a small to medium to sized soma and a small to medium to sized dendritic field as RGB, and cells with a small to medium to sized soma but a medium to large dendritic field RGC. is_a: CL:0000740 ! retinal ganglion cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004117 @@ -24037,8 +24060,8 @@ synonym: "alpha cell" EXACT [] xref: BAMS:1009 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004119 @@ -24050,8 +24073,8 @@ synonym: "retinal ganglion cell B4" EXACT [] xref: BAMS:1047 is_a: CL:0004115 ! retinal ganglion cell B relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004120 @@ -24064,8 +24087,8 @@ synonym: "type I" BROAD [] xref: BAMS:1045 is_a: CL:0004117 ! retinal ganglion cell A relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004121 @@ -24075,8 +24098,8 @@ def: "A retinal ganglion cell B that has a very small but very dense dendritic f xref: BAMS:1048 is_a: CL:0004115 ! retinal ganglion cell B relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004124 @@ -24088,8 +24111,8 @@ synonym: "MTN projecting" RELATED [] synonym: "ON-direction-selective" RELATED [] xref: BAMS:1050 is_a: CL:0003024 ! retinal ganglion cell C inner -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004125 @@ -24098,8 +24121,8 @@ namespace: cell def: "A retinal ganglion cell C inner that has dense dendritic diversity." [PMID:12209831] xref: BAMS:1067 is_a: CL:0003024 ! retinal ganglion cell C inner -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004126 @@ -24108,8 +24131,8 @@ namespace: cell def: "A retinal ganglion cell C outer that has symmetrical and dense dendritic dendritic tree with a large dendritic field." [PMID:12209831] xref: BAMS:1066 is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004137 @@ -24119,8 +24142,8 @@ def: "A retinal ganglion A2 cell with dendrites terminating in S4." [PMID:122098 xref: BAMS:1061 is_a: CL:0004138 ! retinal ganglion cell A2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004138 @@ -24131,8 +24154,8 @@ synonym: "I-1" RELATED [] synonym: "outer alpha retinal ganglion cell" EXACT [] synonym: "type I" RELATED [] is_a: CL:0004117 ! retinal ganglion cell A -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004139 @@ -24142,8 +24165,8 @@ def: "A retinal ganglion A2 cell with dendrites terminating in S2." [PMID:122098 xref: BAMS:1065 is_a: CL:0004138 ! retinal ganglion cell A2 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004161 @@ -24152,8 +24175,8 @@ namespace: cell def: "A cone whose sensitivity measurements have an average spectral peak of 510 nm. These cones are described in rat." [] xref: BAMS:1028 "MB" is_a: CL:0003049 ! M cone cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string property_value: RO:0002175 NCBITaxon:9989 +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004162 @@ -24163,8 +24186,8 @@ def: "A cone whose sensitivity measurements have an average spectral peak of 358 comment: The photopigment curves that provide best fits to...sensitivity measurements have an average spectral peak of 358.2 nm. xref: BAMS:1029 "MB" is_a: CL:0003051 ! UV cone cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string property_value: RO:0002175 NCBITaxon:9989 +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004183 @@ -24174,8 +24197,8 @@ def: "A monostratified retinal ganglion cell with medium soma, sparse dendritic comment: Sixty to eighty neurons with small somata (12 to 24 micrometers in diameter), small dendritic fields (99 to 289 micrometers in diameter), and small axonal diameters (04. to 07. micrometers in diameter) make up Group RGB. We classified cells with a large soma and a large dendritic field as RGA, cells with a small to medium to sized soma and a small to medium to sized dendritic field as RGB, and cells with a small to medium to sized soma but a medium to large dendritic field RGC. xref: BAMS:1049 is_a: CL:0004115 ! retinal ganglion cell B -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004213 @@ -24183,8 +24206,8 @@ name: type 3a cone bipolar cell namespace: cell def: "A type of type 3 cone bipolar cell with distinctive curly dendrites." [PMID:19129389] is_a: CL:0000755 ! type 3 cone bipolar cell (sensu Mus) -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004214 @@ -24192,8 +24215,8 @@ name: type 3b cone bipolar cell namespace: cell def: "A type of type 3 cone bipolar cell with distinctive crescent-shaped dendrites." [PMID:19129389] is_a: CL:0000755 ! type 3 cone bipolar cell (sensu Mus) -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004215 @@ -24201,8 +24224,8 @@ name: type 5a cone bipolar cell namespace: cell def: "A type 5 cone bipolar cell with narrowly stratified post synaptic terminals." [] is_a: CL:0000757 ! type 5 cone bipolar cell (sensu Mus) -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004216 @@ -24210,8 +24233,8 @@ name: type 5b cone bipolar cell namespace: cell def: "A type 5 cone bipolar cell with diffuse axonal branches." [] is_a: CL:0000757 ! type 5 cone bipolar cell (sensu Mus) -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004217 @@ -24222,8 +24245,8 @@ synonym: "A Horizontal Cell" EXACT [] synonym: "H1" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] is_a: CL:0000745 ! retina horizontal cell relationship: CL:4030045 GO:0030424 ! lacks_part axon -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004218 @@ -24234,8 +24257,8 @@ synonym: "B Horizontal Cell" EXACT [] synonym: "H2" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] is_a: CL:0000745 ! retina horizontal cell relationship: RO:0002120 GO:0044316 ! synapsed to cone cell pedicle -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004219 @@ -24249,9 +24272,9 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 relationship: RO:0013001 UBERON:0008927 ! has synaptic IO in region sublaminar layers S1 or S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004220 @@ -24259,8 +24282,8 @@ name: flag amacrine cell namespace: cell def: "An amacrine cell with a small, asymteric dendritic field." [PMID:9620701] is_a: CL:0004251 ! narrow field retinal amacrine cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004221 @@ -24271,8 +24294,8 @@ is_a: CL:0004220 ! flag amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004222 @@ -24284,8 +24307,8 @@ is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004223 @@ -24297,8 +24320,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004224 @@ -24309,8 +24332,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004225 @@ -24321,8 +24344,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004226 @@ -24335,8 +24358,8 @@ intersection_of: bearer_of PATO:0070063 ! monostratified dendrite cell morpholog relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004227 @@ -24348,8 +24371,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 relationship: RO:0013001 UBERON:0009739 ! has synaptic IO in region border of sublaminar layers S3 and S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004228 @@ -24361,8 +24384,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004229 @@ -24373,8 +24396,8 @@ is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004230 @@ -24387,8 +24410,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 relationship: RO:0013001 UBERON:0009852 ! has synaptic IO in region border of sublaminar layers S2 and S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004231 @@ -24399,8 +24422,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004232 @@ -24412,9 +24435,9 @@ subset: human_reference_atlas is_a: CL:0000108 ! cholinergic neuron is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004233 @@ -24426,8 +24449,8 @@ is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004234 @@ -24437,8 +24460,8 @@ def: "An amacrine cell with a medium dendritic field and post-synaptic terminals is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004235 @@ -24449,8 +24472,8 @@ is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004236 @@ -24462,8 +24485,8 @@ is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004237 @@ -24476,8 +24499,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004238 @@ -24488,8 +24511,8 @@ is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 relationship: RO:0013001 UBERON:0009739 ! has synaptic IO in region border of sublaminar layers S3 and S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004239 @@ -24501,8 +24524,8 @@ is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004240 @@ -24511,8 +24534,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S1, and post-synaptic terminals in S1." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004241 @@ -24521,8 +24544,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S2, and post-synaptic terminals in S1." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004242 @@ -24531,8 +24554,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites of this cell type are straight and minimally branched." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004243 @@ -24541,8 +24564,8 @@ namespace: cell def: "An amacrine cell with a wild dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites have spikes, cross over each other, and cover a larger volume than dendrties of W3-1 retinal amacrine cells." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004244 @@ -24551,8 +24574,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S4, and post-synaptic terminals in S4." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004245 @@ -24563,8 +24586,8 @@ is_a: CL:0000850 ! serotonergic neuron is_a: CL:0004253 ! wide field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004246 @@ -24576,8 +24599,8 @@ intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070063 ! monostratified dendrite cell morphology intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004247 @@ -24588,7 +24611,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology relationship: bearer_of PATO:0070062 ! bistratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string [Term] id: CL:0004250 @@ -24599,8 +24622,8 @@ is_a: CL:0000561 ! amacrine cell is_a: CL:0004247 ! bistratified cell intersection_of: CL:0000561 ! amacrine cell intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004251 @@ -24608,8 +24631,8 @@ name: narrow field retinal amacrine cell namespace: cell def: "An amicrine that has a narrow dendritic field." [PMID:9620701] is_a: CL:0000561 ! amacrine cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004252 @@ -24618,9 +24641,9 @@ namespace: cell def: "An amicrine that has a medium dendritic field." [PMID:9620701] subset: human_reference_atlas is_a: CL:0000561 ! amacrine cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004253 @@ -24629,16 +24652,16 @@ namespace: cell def: "An amicrine that has a wide dendritic field." [PMID:9620701] subset: human_reference_atlas is_a: CL:0000561 ! amacrine cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0005000 name: spinal cord interneuron def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. -xref: ZFA:0000778 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0000778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000402 {is_inferred="true"} ! CNS interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002240 ! has soma location spinal cord @@ -24649,7 +24672,7 @@ id: CL:0005001 name: iridoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore." [CL:CVS] comment: Derived from UBERON:0002342 neural crest. -xref: ZFA:0005328 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005328 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -24658,7 +24681,7 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005002 name: xanthoblast def: "A non-terminally differentiated cell that differentiates into a xanthophore." [CL:CVS] -xref: ZFA:0005245 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005245 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -24667,7 +24690,7 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005003 name: leucoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore." [CL:CVS] -xref: ZFA:0005329 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005329 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -24676,7 +24699,7 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005004 name: pigment erythroblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore." [CL:CVS] -xref: ZFA:0005331 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005331 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -24685,7 +24708,7 @@ relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell id: CL:0005005 name: cyanoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore." [CL:CVS] -xref: ZFA:0005332 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -24696,7 +24719,7 @@ name: ionocyte def: "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment." [PMID:17555741, PMID:19268451] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0005323 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -24708,7 +24731,7 @@ synonym: "KA cell" EXACT [] synonym: "KA interneuron" EXACT [PMID:15539490] synonym: "KA neuron" EXACT [PMID:9634146] synonym: "Kolmer-Agduhr cell" EXACT [] -xref: ZFA:0005240 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005240 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005000 ! spinal cord interneuron is_a: CL:0011005 ! GABAergic interneuron @@ -24727,7 +24750,7 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset -xref: ZFA:0005322 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell @@ -24739,7 +24762,7 @@ comment: Intercalated cells are also called “mitochondria-rich cells”, refle subset: cellxgene_subset synonym: "intercalated cell" EXACT [] xref: FMA:86560 -xref: ZFA:0009375 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009375 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -24752,7 +24775,7 @@ comment: Type A intercalated cells are the more abundant type of intercalated ce subset: cellxgene_subset synonym: "type A intercalated cell" EXACT [PMID:25632105] synonym: "type A-IC" EXACT [PMID:25632105] -xref: ZFA:0009376 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009376 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005010 ! renal intercalated cell relationship: capable_of GO:0046717 ! acid secretion @@ -24765,14 +24788,14 @@ synonym: "MCC" RELATED OMO:0003000 [] synonym: "multi-ciliated cell" BROAD [] synonym: "multiciliated cell" BROAD [] synonym: "multiciliated epithelial cell" EXACT [] -xref: ZFA:0005242 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005242 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000067 ! ciliated epithelial cell [Term] id: CL:0005013 name: single ciliated epithelial cell def: "A ciliated epithelial cell with a single cilium." [CL:CVS] -xref: ZFA:0005243 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005243 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000067 ! ciliated epithelial cell [Term] @@ -24780,7 +24803,7 @@ id: CL:0005014 name: auditory epithelial supporting cell def: "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." [CL:CVS, GOC:tfm] synonym: "auditory epithelial support cell" EXACT [] -xref: ZFA:0005244 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005244 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000630 ! supporting cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002491 ! auditory epithelial cell @@ -24810,7 +24833,7 @@ replaced_by: PO:0002002 id: CL:0005018 name: ghrelin secreting cell def: "A cell that secretes ghrelin, the peptide hormone that stimulates hunger." [CL:curator] -xref: ZFA:0005599 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005599 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000167 ! peptide hormone secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0036321 ! ghrelin secretion @@ -24824,7 +24847,7 @@ comment: In mammals the endocrine pancreas is called the Islets of Langerhans. subset: cellxgene_subset subset: human_reference_atlas synonym: "pancreatic E cell" EXACT [] -xref: ZFA:0005598 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005598 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005018 ! ghrelin secreting cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0008024 ! pancreatic endocrine cell @@ -24836,13 +24859,13 @@ id: CL:0005020 name: lymphangioblast def: "Lymphatic progenitor cells." [CL:CVS] comment: Usually express Prox1, or prox1b. -xref: ZFA:0009393 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009393 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell is_a: CL:4033054 ! perivascular cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: adjacent_to UBERON:0004536 ! lymph vasculature relationship: adjacent_to UBERON:0004536 ! lymph vasculature -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 +property_value: terms:contributor https://orcid.org/0000-0002-2244-7917 creation_date: 2012-01-12T04:44:34Z [Term] @@ -24850,10 +24873,10 @@ id: CL:0005021 name: mesenchymal lymphangioblast def: "Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics." [PMID:15624319, PMID:18430230] subset: cellxgene_subset -xref: ZFA:0009394 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009394 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0005020 ! lymphangioblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 +property_value: terms:contributor https://orcid.org/0000-0002-2244-7917 creation_date: 2012-01-12T05:01:22Z [Term] @@ -24862,12 +24885,12 @@ name: vascular lymphangioblast def: "Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells." [CL:CVS] subset: cellxgene_subset synonym: "parachordal lymphangioblast" NARROW [] -xref: ZFA:0009395 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009395 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005020 {is_inferred="true"} ! lymphangioblast intersection_of: CL:0005020 ! lymphangioblast intersection_of: adjacent_to UBERON:0001638 ! vein relationship: adjacent_to UBERON:0001638 ! vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 +property_value: terms:contributor https://orcid.org/0000-0002-2244-7917 creation_date: 2012-01-12T05:21:09Z [Term] @@ -24877,7 +24900,7 @@ def: "Cranial motor neuron which innervates muscles derived from the branchial ( synonym: "branchi motor neuron" EXACT [] synonym: "special visceral motor neuron" EXACT [] xref: PMID:14699587 -xref: ZFA:0005731 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005731 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0015000 ! cranial motor neuron intersection_of: CL:0015000 ! cranial motor neuron intersection_of: RO:0002130 UBERON:0004164 ! has synaptic terminal in branchiomeric muscle @@ -24888,7 +24911,7 @@ id: CL:0005024 name: somatomotor neuron def: "A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic." [ZFIN:CVS] synonym: "somatic motor neuron" EXACT [] -xref: ZFA:0005733 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005733 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron is_a: CL:0000108 ! cholinergic neuron intersection_of: CL:0000100 ! motor neuron @@ -24902,7 +24925,7 @@ def: "A motor neuron that synapses to parasympathetic neurons that innervate tea comment: Note that these neurons do not synapse directly onto muscles subset: cellxgene_subset synonym: "general visceral motor neuron" EXACT [] -xref: ZFA:0005732 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005732 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron relationship: RO:0002120 CL:0011102 ! synapsed to parasympathetic neuron @@ -24924,7 +24947,7 @@ is_a: CL:0000055 ! non-terminally differentiated cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: RO:0002202 CL:0002077 ! develops from ecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T01:27:01Z [Term] @@ -24934,7 +24957,7 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] @@ -24943,7 +24966,7 @@ name: precementoblast def: "Skeletogenic cell that has the potential to develop into a cementoblast." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell relationship: part_of UBERON:0005176 ! tooth enamel organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T04:37:13Z [Term] @@ -24954,19 +24977,19 @@ is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T05:15:11Z [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -24978,7 +25001,7 @@ is_a: BFO:0000002 is_a: CL:0000000 ! cell relationship: part_of UBERON:0002328 ! notochord relationship: RO:0002202 CL:0007006 ! develops from chordamesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:47:31Z [Term] @@ -24988,16 +25011,16 @@ def: "Mesodermal cell that is axially located and gives rise to the cells of the synonym: "axial mesodermal cell" EXACT [] is_a: CL:0000222 ! mesodermal cell relationship: part_of UBERON:0004880 ! chordamesoderm -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:52:41Z [Term] id: CL:0007007 name: notochordal sheath cell def: "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." [CL:MAH] -xref: ZFA:0005744 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005744 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0007005 ! notochordal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T09:26:37Z [Term] @@ -25007,7 +25030,7 @@ def: "Notochordal cell that is inner portion of the notochord and becomes vacuol synonym: "chordablast" EXACT [GO_REF:0000034] synonym: "chordoblast" EXACT [PMID:14574572] is_a: CL:0007005 ! notochordal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T09:29:30Z [Term] @@ -25015,7 +25038,7 @@ id: CL:0007009 name: prechondroblast def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T10:44:01Z [Term] @@ -25031,7 +25054,7 @@ is_a: CL:0011026 ! progenitor cell relationship: part_of UBERON:0008883 ! osteoid relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T10:57:21Z [Term] @@ -25039,7 +25062,7 @@ id: CL:0007011 name: enteric neuron def: "Neuron that is part of the enteric nervous system." [CL:MAH] subset: cellxgene_subset -xref: ZFA:0005775 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005775 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000107 ! autonomic neuron intersection_of: CL:0000540 ! neuron @@ -25047,7 +25070,7 @@ intersection_of: RO:0002100 UBERON:0002005 ! has soma location enteric nervous s relationship: part_of UBERON:0002005 ! enteric nervous system relationship: RO:0002100 UBERON:0002005 ! has soma location enteric nervous system relationship: RO:0002202 CL:0002607 ! develops from migratory enteric neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-28T08:20:31Z [Term] @@ -25068,7 +25091,7 @@ name: obsolete cell line cell def: "OBSOLETE: A cultured cell that has been passaged at least one time in culture." [ReO:mhb] comment: Obsoleted in July 2013 and replaced by the CLO 'cell line cell' class, as a result of CLO-OBI-CL alignment efforts.\n\nCovers cells actively being cultured or stored in a quiescent state for future use. synonym: "passaged cultured cell" EXACT [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 is_obsolete: true replaced_by: CLO:0000001 creation_date: 2012-11-28T11:54:59Z @@ -25080,7 +25103,7 @@ def: "OBSOLETE: A cell line cell that is expected to be capable of replicating a comment: Obsoleted in July 2013 and replaced by the CLO 'mortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts.\n\nCovers cells actively being cultured or stored in a quiescent state for future use. synonym: "finite cell line cell" EXACT [] synonym: "primary cell line cell" RELATED [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 is_obsolete: true replaced_by: CLO:0000018 creation_date: 2012-11-28T11:56:20Z @@ -25090,10 +25113,10 @@ id: CL:0007016 name: adaxial cell def: "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." [PMID:8951054] comment: In teleosts, adaxial cells give rise to slow muscle myoblasts. -xref: ZFA:0000003 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0000003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell relationship: part_of UBERON:0003059 ! presomitic mesoderm -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-12-30T12:43:15Z [Term] @@ -25104,7 +25127,7 @@ comment: Taxon specificity not yet fully known, but are known in anuran larvae b is_a: CL:0000206 ! chemoreceptor cell relationship: has_part GO:0005902 ! microvillus relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007018 @@ -25114,21 +25137,21 @@ comment: Taxon specificity not clear -present in embryonic anurans. is_a: CL:0000064 ! ciliated cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007019 name: epidermal mucus secreting cell comment: taxon specificity not clear. Appears in early larval stages of anurans and persists after metamorphosis. is_a: CL:0000319 ! mucus secreting cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007020 name: bottle cell def: "Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians." [PMID:3197630] is_a: CL:0000007 ! early embryonic cell (metazoa) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007021 @@ -25140,17 +25163,17 @@ synonym: "club cell (zebrafish)" EXACT [https://github.com/obophenotype/cell-ont is_a: CL:0000151 ! secretory cell is_a: CL:0000473 ! defensive cell relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007022 name: micropylar cell def: "A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg." [PMID:18582455, ZFA:0005239] synonym: "plug cell" EXACT [] -xref: ZFA:0005239 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: part_of UBERON:0001305 ! ovarian follicle -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007023 @@ -25158,7 +25181,7 @@ name: flask cell def: "Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis." [DOI:10.1007/BF00717048] is_a: CL:0000000 ! cell relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0008000 @@ -25203,7 +25226,7 @@ intersection_of: has_part GO:0030017 ! sarcomere id: CL:0008004 name: somatic muscle cell def: "A muscle cell that is part of some somatic muscle." [GOC:dos] -xref: FBbt:00005073 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell [Term] @@ -25228,7 +25251,7 @@ is_a: CL:0008018 ! somatic muscle myoblast id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -25395,7 +25418,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0008025 name: noradrenergic neuron def: "A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter." [GOC:dos] -xref: ZFA:0005873 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005873 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000459 ! noradrenergic cell is_a: CL:4033050 ! catecholaminergic neuron intersection_of: CL:0000540 ! neuron @@ -25406,7 +25429,7 @@ relationship: capable_of GO:0061533 ! norepinephrine secretion, neurotransmissio id: CL:0008026 name: open tracheal system tracheocyte def: "An epithelial cell that is part of the epithelium of a tracheal tube in an open tracheal system, such as that found in insects." [GOC:dos] -xref: FBbt:00005038 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0003127 ! open tracheal system trachea @@ -25417,7 +25440,7 @@ id: CL:0008027 name: rod bipolar cell (sensu Mus) def: "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells. These neurons have axons that arborize and synapse to targets in inner plexiform layers 4 and 5 and depolarize in response to light." [] is_a: CL:0000751 ! rod bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-06-29T11:05:22Z [Term] @@ -25428,7 +25451,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-09T19:12:36Z [Term] @@ -25436,7 +25459,7 @@ id: CL:0008029 name: obsolete inhibitory neuron comment: Consider GABAergic neuron or inhibitory interneuron instead. Do note that not all GABAergic neurons are inhibitory (see PMID:12209121) and replacing inhibitory neuron with GABAergic neuron should be done with caution. relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1540 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 is_obsolete: true creation_date: 2017-07-12T11:10:52Z @@ -25445,7 +25468,7 @@ id: CL:0008030 name: obsolete excitatory neuron comment: Consider using glutamatergic neuron instead. Do note that not all glutamatergic neurons are excitatory and replacing excitatory neuron with glutamatergic neuron should be done with caution. relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1540 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 is_obsolete: true creation_date: 2017-07-12T11:11:06Z @@ -25485,7 +25508,7 @@ is_a: CL:2000078 ! placental pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0002450 ! decidua relationship: part_of UBERON:0002450 ! decidua -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T11:45:57Z [Term] @@ -25495,10 +25518,10 @@ def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0005944 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005944 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033054 ! perivascular cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T17:33:55Z [Term] @@ -25510,7 +25533,7 @@ is_a: CL:0008034 ! mural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0010523 ! microcirculatory vessel relationship: part_of UBERON:0010523 ! microcirculatory vessel -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T17:37:00Z [Term] @@ -25523,8 +25546,8 @@ subset: human_reference_atlas synonym: "EVT" EXACT [PMID:31049600] synonym: "extravillous cytotrophloblast" EXACT [] is_a: CL:0000351 ! trophoblast cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-03-02T08:45:06Z [Term] @@ -25545,7 +25568,7 @@ def: "A large, multipolar lower motor neuron of the brainstem and spinal cord th synonym: "alpha motoneuron" EXACT [] is_a: CL:0008039 ! lower motor neuron relationship: RO:0002120 CL:0008046 ! synapsed to extrafusal muscle fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-23T20:16:26Z [Term] @@ -25556,9 +25579,18 @@ xref: FMA:84632 is_a: BFO:0000002 is_a: CL:0005024 ! somatomotor neuron relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-23T20:22:07Z +[Term] +id: CL:0008040 +name: squamous endothelial cell of venule +def: "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [] {comment="GOC:tfm"} +is_a: CL:0002653 ! squamous endothelial cell +is_a: CL:1000414 ! endothelial cell of venule +property_value: dc:date "2024-07-03T19:52:47Z" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 + [Term] id: CL:0008046 name: extrafusal muscle fiber @@ -25568,7 +25600,7 @@ xref: TH:H3.03.00.0.00007 is_a: CL:0008002 ! skeletal muscle fiber disjoint_from: CL:0008047 ! intrafusal muscle fiber relationship: RO:0002103 CL:0008038 ! synapsed by alpha motor neuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-26T21:06:15Z [Term] @@ -25582,7 +25614,7 @@ is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: part_of UBERON:0003718 ! muscle spindle relationship: part_of UBERON:0003718 ! muscle spindle -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-26T21:07:01Z [Term] @@ -25593,7 +25625,7 @@ is_a: CL:0000100 ! motor neuron is_a: CL:0000679 ! glutamatergic neuron relationship: RO:0002120 CL:0008039 ! synapsed to lower motor neuron relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-28T09:41:48Z [Term] @@ -25606,9 +25638,9 @@ is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuro relationship: bearer_of PATO:0070017 ! standard pyramidal morphology relationship: RO:0002100 UBERON:0022315 ! has soma location primary motor cortex layer 5 relationship: RO:0002101 UBERON:0002707 ! fasciculates with corticospinal tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 -property_value: http://xmlns.com/foaf/0.1/depiction "https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg" xsd:string +property_value: foaf:depiction "https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg" xsd:string property_value: RO:0002175 NCBITaxon:9443 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-28T09:52:58Z [Term] @@ -25683,7 +25715,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell is_a: CL:1001598 ! small intestine glandular cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009007 @@ -25696,7 +25728,7 @@ is_a: CL:0000865 ! gastrointestinal tract (lamina propria) macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine relationship: part_of UBERON:0001238 ! lamina propria of small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009008 @@ -25709,7 +25741,7 @@ is_a: CL:0000865 ! gastrointestinal tract (lamina propria) macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine relationship: part_of UBERON:0011189 ! lamina propria of large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009009 @@ -25725,8 +25757,8 @@ is_a: CL:0000510 ! paneth cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0000397 ! colonic epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009010 @@ -25741,7 +25773,7 @@ synonym: "transit-amplifying cell" EXACT [] is_a: BFO:0000002 is_a: CL:0000000 ! cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009011 @@ -25761,8 +25793,8 @@ intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon relationship: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009012 @@ -25780,7 +25812,7 @@ intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009013 @@ -25792,7 +25824,7 @@ synonym: "HHyP cell" EXACT [] is_a: CL:0011026 ! progenitor cell relationship: part_of UBERON:8410003 ! ductal plate relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009014 @@ -25805,7 +25837,7 @@ is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0001211 ! Peyer's patch relationship: part_of UBERON:0001211 ! Peyer's patch -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009015 @@ -25816,7 +25848,7 @@ is_a: CL:0000442 ! follicular dendritic cell intersection_of: CL:0000442 ! follicular dendritic cell intersection_of: part_of UBERON:0001211 ! Peyer's patch relationship: part_of UBERON:0001211 ! Peyer's patch -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009016 @@ -25832,8 +25864,8 @@ is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001984 ! crypt of Lieberkuhn of large intestine relationship: part_of UBERON:0001984 ! crypt of Lieberkuhn of large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009017 @@ -25848,7 +25880,7 @@ is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009018 @@ -25862,8 +25894,8 @@ is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine relationship: part_of UBERON:0011189 ! lamina propria of large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009019 @@ -25876,7 +25908,7 @@ is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0002681 ! kidney cortical cell intersection_of: part_of UBERON:0009871 ! nephrogenic zone relationship: part_of UBERON:0009871 ! nephrogenic zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009020 @@ -25890,7 +25922,7 @@ is_a: CL:0002203 ! brush cell of epithelium proper of large intestine is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009021 @@ -25901,7 +25933,7 @@ is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine relationship: part_of UBERON:0011189 ! lamina propria of large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009022 @@ -25913,7 +25945,7 @@ is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine relationship: part_of UBERON:0001238 ! lamina propria of small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009023 @@ -25927,7 +25959,7 @@ is_a: CL:0009014 ! Peyer's patch lymphocyte intersection_of: CL:0002419 ! mature T cell intersection_of: part_of UBERON:0003454 ! small intestine Peyer's patch relationship: part_of UBERON:0003454 ! small intestine Peyer's patch -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009024 @@ -25938,7 +25970,7 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009025 @@ -25950,7 +25982,7 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009026 @@ -25964,7 +25996,7 @@ is_a: CL:0000584 ! enterocyte is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009027 @@ -25979,7 +26011,7 @@ intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix relationship: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix relationship: RO:0002202 CL:0009028 ! develops from intestinal crypt stem cell of appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009028 @@ -25996,7 +26028,7 @@ is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix relationship: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009029 @@ -26010,7 +26042,7 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009030 @@ -26024,7 +26056,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell is_a: CL:1001585 ! appendix glandular cell intersection_of: CL:1001516 ! intestinal enteroendocrine cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009031 @@ -26039,7 +26071,7 @@ is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009032 @@ -26054,7 +26086,7 @@ is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009033 @@ -26069,7 +26101,7 @@ is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009034 @@ -26084,7 +26116,7 @@ is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009035 @@ -26098,7 +26130,7 @@ intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001154 ! vermiform appendix intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009036 @@ -26113,7 +26145,7 @@ is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009037 @@ -26127,7 +26159,7 @@ is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0010420 ! lymph node germinal center mantle zone relationship: part_of UBERON:0010420 ! lymph node germinal center mantle zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009038 @@ -26141,7 +26173,7 @@ is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009039 @@ -26154,7 +26186,7 @@ is_a: CL:1000320 ! large intestine goblet cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009040 @@ -26166,7 +26198,7 @@ is_a: CL:0009021 ! stromal cell of lamina propria of large intestine intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0007177 ! lamina propria of mucosa of colon relationship: part_of UBERON:0007177 ! lamina propria of mucosa of colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009041 @@ -26179,7 +26211,7 @@ is_a: CL:0002203 ! brush cell of epithelium proper of large intestine is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009042 @@ -26192,7 +26224,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009043 @@ -26204,7 +26236,7 @@ is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009044 @@ -26222,7 +26254,7 @@ is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine relationship: part_of UBERON:0001238 ! lamina propria of small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009045 @@ -26234,7 +26266,7 @@ is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus relationship: part_of UBERON:0009744 ! lymph node medullary sinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009046 @@ -26246,7 +26278,7 @@ is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus relationship: part_of UBERON:0009744 ! lymph node medullary sinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009047 @@ -26260,7 +26292,7 @@ is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus relationship: part_of UBERON:0009744 ! lymph node medullary sinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009048 @@ -26273,7 +26305,7 @@ is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009049 @@ -26287,7 +26319,7 @@ is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:8410038 ! high endothelial venule of lymph node relationship: part_of UBERON:8410038 ! high endothelial venule of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009050 @@ -26299,7 +26331,7 @@ is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009051 @@ -26311,7 +26343,7 @@ is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009052 @@ -26323,7 +26355,7 @@ is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009053 @@ -26335,7 +26367,7 @@ intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009054 @@ -26347,7 +26379,7 @@ is_a: CL:1000360 ! microfold cell of epithelium proper of large intestine intersection_of: CL:0000682 ! M cell of gut intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009055 @@ -26360,7 +26392,7 @@ is_a: CL:0002658 ! glandular cell of the large intestine intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009056 @@ -26372,7 +26404,7 @@ is_a: CL:0009010 ! transit amplifying cell intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009057 @@ -26384,7 +26416,7 @@ is_a: CL:1000320 ! large intestine goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009058 @@ -26397,7 +26429,7 @@ is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009059 @@ -26412,7 +26444,7 @@ is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus relationship: part_of UBERON:0009744 ! lymph node medullary sinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009060 @@ -26425,7 +26457,7 @@ is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: part_of UBERON:8410065 ! lymph node follicle marginal zone relationship: part_of UBERON:8410065 ! lymph node follicle marginal zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009061 @@ -26438,7 +26470,7 @@ is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009062 @@ -26452,7 +26484,7 @@ is_a: CL:0002038 ! T follicular helper cell intersection_of: CL:0002038 ! T follicular helper cell intersection_of: part_of UBERON:0009039 ! lymph node germinal center relationship: part_of UBERON:0009039 ! lymph node germinal center -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009063 @@ -26465,7 +26497,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009064 @@ -26479,7 +26511,7 @@ is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:8410066 ! lymph node paracortex relationship: part_of UBERON:8410066 ! lymph node paracortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009065 @@ -26491,7 +26523,7 @@ is_a: CL:0002203 ! brush cell of epithelium proper of large intestine intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009066 @@ -26505,7 +26537,7 @@ is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000240 ! stratified squamous epithelial cell intersection_of: part_of UBERON:0000159 ! anal canal relationship: part_of UBERON:0000159 ! anal canal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009067 @@ -26517,7 +26549,7 @@ synonym: "vacuolated enterocyte" BROAD [] is_a: CL:0000584 ! enterocyte is_a: CL:0002254 ! epithelial cell of small intestine relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009068 @@ -26526,8 +26558,8 @@ def: "An unconventional T lymphocyte population within the thymic medulla that i subset: human_reference_atlas is_a: CL:0000893 ! thymocyte relationship: part_of UBERON:0002124 ! medulla of thymus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009069 @@ -26536,8 +26568,8 @@ def: "An unconventional T lymphocyte population within the thymic medulla that e subset: human_reference_atlas is_a: CL:0000893 ! thymocyte relationship: part_of UBERON:0002124 ! medulla of thymus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009070 @@ -26546,8 +26578,8 @@ def: "A thymic epithelial cell located at the corticomedullary junction." [PMID: subset: human_reference_atlas is_a: CL:0002293 ! epithelial cell of thymus relationship: part_of UBERON:0003988 ! thymus corticomedullary boundary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009071 @@ -26556,8 +26588,8 @@ def: "A thymic medullary epithelial cell considered to be a pre-AIRE mTEC popula subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009072 @@ -26566,8 +26598,8 @@ def: "A thymic medullary epithelial cell that expresses AIRE or other canonical subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009073 @@ -26576,8 +26608,8 @@ def: "A thymic medullary epithelial cell considered to be a post-AIRE cell. This subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009074 @@ -26587,8 +26619,8 @@ subset: human_reference_atlas synonym: "thymic tuft cell" BROAD [] is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009075 @@ -26597,8 +26629,8 @@ def: "A thymic medullary epithelial cell that expresses muscle-specific biomarke subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009076 @@ -26607,8 +26639,8 @@ def: "A thymic medullary epithelial cell that expresses neuroendocrine biomarker subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell relationship: part_of UBERON:0003846 ! thymus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009077 @@ -26617,8 +26649,8 @@ def: "A thymic epithelial cell located within the subcapsular region of the thym subset: human_reference_atlas is_a: CL:0002364 ! cortical thymic epithelial cell relationship: part_of UBERON:0006936 ! thymus subcapsular epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009078 @@ -26628,8 +26660,8 @@ subset: human_reference_atlas synonym: "thymic capsular fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002122 ! capsule of thymus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009079 @@ -26639,8 +26671,8 @@ subset: human_reference_atlas synonym: "thymic interlobular fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0004791 ! thymus trabecula -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009080 @@ -26655,8 +26687,8 @@ is_a: CL:0002254 ! epithelial cell of small intestine is_a: CL:0019032 ! intestinal tuft cell intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009081 @@ -26665,19 +26697,20 @@ def: "The human equivalent of a DN2 thymocyte; typically contains two phases, in comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas is_a: CL:0002489 ! double negative thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-11-25T09:26:32Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-11-25T09:26:32Z" xsd:dateTime [Term] id: CL:0009082 name: committed double negative thymocyte (Homo sapiens) def: "The human equivalent of a DN3 thymocyte; these thymocytes finish the process of beta selection." [PMID:32304633] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. +subset: human_reference_atlas is_a: CL:0002489 ! double negative thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-11-25T09:30:45Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-11-25T09:30:45Z" xsd:dateTime [Term] id: CL:0009083 @@ -26686,9 +26719,9 @@ def: "The human equivalent of a DN4 thymocyte." [PMID:32304633] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas is_a: CL:0002489 ! double negative thymocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-11-25T09:32:13Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-11-25T09:32:13Z" xsd:dateTime [Term] id: CL:0009084 @@ -26702,9 +26735,9 @@ is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002451 ! endometrial gland relationship: part_of UBERON:0002451 ! endometrial gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-11-30T16:13:30Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-11-30T16:13:30Z" xsd:dateTime [Term] id: CL:0009085 @@ -26712,8 +26745,8 @@ name: colony forming unit – Hill cell def: "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. They may form discrete colonies." [WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016#Colony_forming_unit_–_Hill] synonym: "CFU-Hill" EXACT [] is_a: CL:0002619 ! adult endothelial progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-18T09:55:33Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-18T09:55:33Z" xsd:dateTime [Term] id: CL:0009086 @@ -26722,13 +26755,13 @@ def: "An endothelial cell that is part of a respiratory system lymphatic vessel. subset: human_reference_atlas subset: location_grouping xref: EFO:0010667 -is_a: CL:0000115 ! endothelial cell +is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003456 ! respiratory system lymphatic vessel relationship: part_of UBERON:0003529 ! respiratory system lymphatic vessel endothelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-03T14:00:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-03T14:00:44Z" xsd:dateTime [Term] id: CL:0009087 @@ -26737,16 +26770,16 @@ def: "An extravillous trophoblast that is polynuclear." [https://orcid.org/0000- synonym: "fused EVT" EXACT [] xref: EFO:0010712 is_a: CL:0008036 ! extravillous trophoblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-03T14:37:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-03T14:37:32Z" xsd:dateTime [Term] id: CL:0009088 name: circulating angiogenic cell def: "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. These cells do not form colonies." [WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016#Circulating_angiogenic_cell] is_a: CL:0002619 ! adult endothelial progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-18T10:12:57Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-18T10:12:57Z" xsd:dateTime [Term] id: CL:0009089 @@ -26762,9 +26795,9 @@ is_a: CL:0000669 ! pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-03T17:13:33Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-03T17:13:33Z" xsd:dateTime [Term] id: CL:0009090 @@ -26773,8 +26806,8 @@ def: "An adult endothelial progenitor cell that is resident of adult vasculature synonym: "ECFC" EXACT [] is_a: CL:0002619 ! adult endothelial progenitor cell relationship: part_of UBERON:0004537 ! blood vasculature -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-18T10:15:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-18T10:15:32Z" xsd:dateTime [Term] id: CL:0009091 @@ -26784,8 +26817,8 @@ synonym: "stem Leydig cell" EXACT [] is_a: CL:0000034 ! stem cell is_a: CL:4030031 ! interstitial cell relationship: part_of UBERON:0005212 ! Leydig cell region of testis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-18T14:09:25Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-18T14:09:25Z" xsd:dateTime [Term] id: CL:0009092 @@ -26796,11 +26829,11 @@ subset: location_grouping synonym: "placental endothelial cell" EXACT [] xref: EFO:0010708 is_a: CL:0000115 ! endothelial cell -is_a: CL:0002577 ! placental epithelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-13T13:53:01Z" xsd:dateTime +relationship: part_of UBERON:0001987 ! placenta +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-13T13:53:01Z" xsd:dateTime [Term] id: CL:0009093 @@ -26813,8 +26846,8 @@ is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-13T13:56:42Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-13T13:56:42Z" xsd:dateTime [Term] id: CL:0009094 @@ -26823,12 +26856,12 @@ def: "An endothelial cell that is part of a hepatic portal vein." [https://orcid subset: location_grouping synonym: "portal endothelial cell" BROAD [] xref: EFO:0010704 -is_a: CL:0000115 ! endothelial cell +is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001639 ! hepatic portal vein relationship: part_of UBERON:0001639 ! hepatic portal vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-13T14:01:05Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-13T14:01:05Z" xsd:dateTime [Term] id: CL:0009095 @@ -26842,8 +26875,8 @@ is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-13T14:39:25Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-13T14:39:25Z" xsd:dateTime [Term] id: CL:0009096 @@ -26862,9 +26895,9 @@ is_a: CL:0002252 ! epithelial cell of esophagus intersection_of: CL:0000238 ! non keratinizing barrier epithelial cell intersection_of: part_of UBERON:0006920 ! esophagus squamous epithelium relationship: part_of UBERON:0006920 ! esophagus squamous epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-21T15:00:13Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-21T15:00:13Z" xsd:dateTime [Term] id: CL:0009097 @@ -26874,8 +26907,8 @@ is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-21T15:39:10Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-21T15:39:10Z" xsd:dateTime [Term] id: CL:0009098 @@ -26887,8 +26920,8 @@ intersection_of: RO:0002488 UBERON:0000092 ! existence starts during post-embryo intersection_of: RO:0002492 UBERON:0007221 ! existence ends during neonate stage relationship: RO:0002488 UBERON:0000092 ! existence starts during post-embryonic stage relationship: RO:0002492 UBERON:0007221 ! existence ends during neonate stage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-21T15:43:16Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-21T15:43:16Z" xsd:dateTime [Term] id: CL:0009099 @@ -26898,8 +26931,8 @@ subset: cellxgene_subset synonym: "fibro/adipogenic progenitor" EXACT [] is_a: CL:0008019 ! mesenchymal cell is_a: CL:0011026 ! progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-21T16:50:02Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-21T16:50:02Z" xsd:dateTime [Term] id: CL:0009100 @@ -26911,9 +26944,9 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001279 ! portal triad relationship: part_of UBERON:0001279 ! portal triad -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-17T12:00:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-17T12:00:44Z" xsd:dateTime [Term] id: CL:0009101 @@ -26921,9 +26954,9 @@ name: fibroblastic reticular cell def: "A reticular cell involved in directing B cells and T cells to specific regions within a tissue." [] is_a: CL:0000186 ! myofibroblast cell is_a: CL:0000432 ! reticular cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-21T15:20:33Z" xsd:dateTime property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-21T15:20:33Z" xsd:dateTime [Term] id: CL:0009102 @@ -26934,10 +26967,10 @@ is_a: CL:0009101 ! fibroblastic reticular cell intersection_of: CL:0009101 ! fibroblastic reticular cell intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-21T15:24:01Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-21T15:24:01Z" xsd:dateTime [Term] id: CL:0009103 @@ -26947,10 +26980,10 @@ subset: human_reference_atlas synonym: "marginal reticular cell" BROAD [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell relationship: RO:0001025 UBERON:0005463 ! located in subcapsular sinus of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-21T15:59:56Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-21T15:59:56Z" xsd:dateTime [Term] id: CL:0009104 @@ -26962,10 +26995,10 @@ synonym: "lymph node germinal center dark zone fibroblastic reticular cell" EXAC synonym: "T-B boundary reticular cell" RELATED [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell relationship: part_of UBERON:8410053 ! lymph node germinal center dark zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-21T16:55:46Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-21T16:55:46Z" xsd:dateTime [Term] id: CL:0009105 @@ -26976,10 +27009,10 @@ synonym: "interfollicular reticular cell" RELATED [PMID:34256989] synonym: "lymph node T cell domain fibroblastic reticular cell" EXACT [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell relationship: part_of UBERON:0010417 ! lymph node T cell domain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-21T17:19:56Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-21T17:19:56Z" xsd:dateTime [Term] id: CL:0009106 @@ -26992,10 +27025,10 @@ synonym: "MedRC" RELATED OMO:0003000 [] synonym: "medullary reticular cell of lymph node" EXACT [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell relationship: part_of UBERON:0002007 ! medulla of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-22T09:03:15Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-22T09:03:15Z" xsd:dateTime [Term] id: CL:0009107 @@ -27003,12 +27036,11 @@ name: lymphatic endothelial cell of subcapsular sinus ceiling def: "A lymphatic endothelial cell located in the subcapsular sinus ceiling of a lymph node. In human, it's characterized by a unique marker expression (NT5e+ and Caveolin-1+)." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas synonym: "lymphatic endothelial cell of subcapsular sinus ceiling of lymph node" EXACT [] -is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:8410071 ! subcapsular sinus ceiling -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-22T10:30:28Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-22T10:30:28Z" xsd:dateTime [Term] id: CL:0009108 @@ -27016,12 +27048,11 @@ name: lymphatic endothelial cell of subcapsular sinus floor def: "A lymphatic endothelial cell located in the subcapsular sinus floor of a lymph node. In human, it's characterized by a unique marker expression (TNFRSF9+)." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas synonym: "lymphatic endothelial cell of subcapsular sinus floor of lymph node" EXACT [] -is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:8410072 ! subcapsular sinus floor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-22T10:39:28Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-22T10:39:28Z" xsd:dateTime [Term] id: CL:0009109 @@ -27030,12 +27061,11 @@ def: "A lymphatic endothelial cell located in a lymph node trabecula." [https:// subset: human_reference_atlas synonym: "lymphatic endothelial cell of lymph node trabecula" EXACT [] synonym: "lymphatic endothelial cell of trabeculae" EXACT [] -is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:0002195 ! trabecula of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-23T15:08:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-23T15:08:44Z" xsd:dateTime [Term] id: CL:0009110 @@ -27043,12 +27073,11 @@ name: lymphatic endothelial cell of medulla ceiling def: "A lymphatic endothelial cell located in the ceiling part of a lymph node medulla." [https://orcid.org/0000-0001-7655-4833, PMID:31402260, PMID:32426372] subset: human_reference_atlas synonym: "lymphatic endothelial cell of lymph node medulla ceiling" EXACT [] -is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell relationship: part_of UBERON:0002007 ! medulla of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-23T15:13:30Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-23T15:13:30Z" xsd:dateTime [Term] id: CL:0009111 @@ -27059,9 +27088,9 @@ subset: human_reference_atlas synonym: "lymph node centrocyte" EXACT [] is_a: CL:0000844 ! germinal center B cell relationship: part_of UBERON:8410052 ! lymph node germinal center light zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-24T09:03:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-24T09:03:44Z" xsd:dateTime [Term] id: CL:0009112 @@ -27072,9 +27101,9 @@ subset: human_reference_atlas synonym: "lymph node centroblast" EXACT [] is_a: CL:0000844 ! germinal center B cell relationship: part_of UBERON:8410053 ! lymph node germinal center dark zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-24T09:12:41Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-24T09:12:41Z" xsd:dateTime [Term] id: CL:0009113 @@ -27085,9 +27114,9 @@ subset: human_reference_atlas synonym: "follicular regulatory T cell" EXACT [] is_a: CL:0000815 ! regulatory T cell relationship: part_of UBERON:0001744 ! lymphoid tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-24T09:36:29Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-24T09:36:29Z" xsd:dateTime [Term] id: CL:0009114 @@ -27096,24 +27125,23 @@ def: "A B cell found in the perisinusoidal area of a lymph node. In humans, mono subset: human_reference_atlas is_a: CL:0000236 ! B cell relationship: part_of UBERON:8410066 ! lymph node paracortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-24T10:18:12Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-24T10:18:12Z" xsd:dateTime [Term] id: CL:0009115 name: lymph node lymphatic vessel endothelial cell def: "An endothelial cell located in a lymph node lymphatic vessel." [https://orcid.org/0000-0001-7655-4833] subset: human_reference_atlas -is_a: CL:0000115 ! endothelial cell +is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0001473 ! lymphatic vessel relationship: part_of UBERON:0000029 ! lymph node -relationship: part_of UBERON:0001473 ! lymphatic vessel -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009116 @@ -27124,7 +27152,7 @@ synonym: "luminal progenitor cell" BROAD [] synonym: "progenitor cell of luminal mammary epithelium" EXACT [] is_a: CL:0011026 ! progenitor cell relationship: part_of UBERON:0001911 ! mammary gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0010000 @@ -27142,7 +27170,7 @@ is_a: CL:0000499 ! stromal cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010002 @@ -27153,7 +27181,7 @@ is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001310 ! umbilical artery relationship: part_of UBERON:0001310 ! umbilical artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010003 @@ -27163,11 +27191,11 @@ comment: May be merged with pneumocyte in future subset: cellxgene_subset synonym: "alveolus of lung epithelial cell" EXACT [] xref: MESH:D056809 -is_a: CL:0000082 ! epithelial cell of lung +is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002299 ! alveolus of lung relationship: part_of UBERON:0002299 ! alveolus of lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010004 @@ -27178,7 +27206,7 @@ is_a: CL:0000842 ! mononuclear cell is_a: CL:1001610 ! bone marrow hematopoietic cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010005 @@ -27267,9 +27295,9 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1359" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:0010013 @@ -27372,7 +27400,7 @@ xref: ILX:0107463 is_a: CL:0000165 ! neuroendocrine cell is_a: CL:2000029 ! central nervous system neuron relationship: RO:0002100 UBERON:0001898 ! has soma location hypothalamus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:0011004 @@ -27381,7 +27409,7 @@ def: "A vetebrate lens cell that is any of the elongated, tightly packed cells t subset: cellxgene_subset subset: human_reference_atlas synonym: "lens fibre cell" EXACT [] -xref: ZFA:0009401 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009401 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002222 ! vertebrate lens cell property_value: RO:0002175 NCBITaxon:9606 @@ -27458,21 +27486,21 @@ is_a: CL:0000219 ! motile cell intersection_of: CL:0000019 ! sperm intersection_of: capable_of GO:0097722 ! sperm motility relationship: capable_of GO:0097722 ! sperm motility -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011014 name: non-motile sperm cell def: "A sperm cell that is not cabaple of motion (motility)." [PMID:30612620] is_a: CL:0000019 ! sperm -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011015 name: amoeboid sperm cell def: "A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system." [PMID:17708982] is_a: CL:0011013 ! motile sperm cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011016 @@ -27482,14 +27510,14 @@ is_a: CL:0011013 ! motile sperm cell intersection_of: CL:0011013 ! motile sperm cell intersection_of: capable_of GO:0030317 ! flagellated sperm motility relationship: capable_of GO:0030317 ! flagellated sperm motility -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011017 name: vagal neural crest cell def: "Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations." [PMID:22016183] is_a: CL:0011012 ! neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011018 @@ -27499,7 +27527,7 @@ synonym: "LTi" EXACT [] synonym: "lymphoid tissue inducer cell" EXACT [] is_a: CL:0001071 ! group 3 innate lymphoid cell relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011019 @@ -27511,7 +27539,7 @@ is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002348 ! epicardium relationship: part_of UBERON:0002348 ! epicardium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011020 @@ -27519,7 +27547,7 @@ name: neural progenitor cell def: "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew." [PMID:30574073] subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011021 @@ -27529,7 +27557,7 @@ is_a: CL:0011022 ! fibroblast of skin of back intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0009015 ! upper back skin relationship: part_of UBERON:0009015 ! upper back skin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011022 @@ -27539,7 +27567,7 @@ is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001068 ! skin of back relationship: part_of UBERON:0001068 ! skin of back -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011023 @@ -27553,7 +27581,7 @@ intersection_of: RO:0001000 CL:0000097 ! derives from mast cell intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha relationship: RO:0001000 CL:0000097 ! derives from mast cell relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011024 @@ -27567,16 +27595,16 @@ is_a: CL:0002489 ! double negative thymocyte intersection_of: CL:0002489 ! double negative thymocyte intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0050777 ! negative regulation of immune response -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011025 name: exhausted T cell +def: "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential." [PMID:26544946] subset: cellxgene_subset -synonym: "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential." EXACT [PMID:26544946] synonym: "Tex cell" EXACT [] is_a: CL:0000911 ! effector T cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011026 @@ -27588,7 +27616,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011027 @@ -27600,16 +27628,16 @@ is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:1001609 ! muscle fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011028 name: olfactory ensheathing cell -synonym: "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons." EXACT [PMID:22456085] +def: "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons." [PMID:22456085] synonym: "OEC" EXACT [] xref: BTO:0002771 is_a: CL:0000125 ! glial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011029 @@ -27620,7 +27648,7 @@ synonym: "nematocyte" EXACT [] is_a: CL:0000151 ! secretory cell relationship: has_part GO:0042151 ! nematocyst relationship: RO:0002162 NCBITaxon:6073 ! in taxon Cnidaria -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011030 @@ -27632,7 +27660,7 @@ is_a: CL:2000008 ! microvascular endothelial cell is_a: CL:2000010 ! dermis blood vessel endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0002067 ! dermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011031 @@ -27642,8 +27670,8 @@ subset: human_reference_atlas synonym: "MDDC cell" EXACT [] is_a: CL:0000782 ! myeloid dendritic cell relationship: RO:0002202 CL:0000576 ! develops from monocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011032 @@ -27654,7 +27682,7 @@ synonym: "immature enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, P synonym: "LRE" EXACT [] synonym: "vacuolated enterocyte" BROAD [] is_a: CL:0000584 ! enterocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011100 @@ -27676,7 +27704,7 @@ relationship: part_of UBERON:0003124 ! chorion membrane id: CL:0011102 name: parasympathetic neuron def: "Parasympathetic neurons are part of the parasympathetic nervous sysem and the cell bodies lie in the brain and sacral region of the spinal cord. The neurons are mainly cholinergic." [GOC:NV, isbn:0080923437] -xref: ZFA:0005776 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005776 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000107 ! autonomic neuron [Term] @@ -27685,7 +27713,7 @@ name: sympathetic neuron def: "Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides." [GOC:NV, isbn:0080923437] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0005777 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005777 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000107 ! autonomic neuron property_value: RO:0002175 NCBITaxon:9606 @@ -27746,7 +27774,7 @@ id: CL:0011109 name: hypocretin-secreting neuron def: "A neuron that releases hypocretin as a neurotransmitter." [GOC:NV, PMID:23848055] synonym: "orexin" EXACT [] -xref: ZFA:0005778 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -27757,7 +27785,7 @@ relationship: capable_of GO:0061585 ! orexin secretion, neurotransmission id: CL:0011110 name: histaminergic neuron def: "Neuron that secretes histamine." [GOC:NV, PMID:22677810] -xref: FBbt:00007367 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007367 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000540 ! neuron is_a: CL:0002274 ! histamine secreting cell intersection_of: CL:0000540 ! neuron @@ -27819,8 +27847,8 @@ is_a: CL:2000005 ! brain macroglial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0001890 ! forebrain relationship: part_of UBERON:0001890 ! forebrain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3837-8864 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-3837-8864 [Term] id: CL:0012001 @@ -27833,8 +27861,8 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0001890 ! has soma location forebrain relationship: RO:0002100 UBERON:0001890 ! has soma location forebrain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3837-8864 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-3837-8864 [Term] id: CL:0013000 @@ -27852,7 +27880,7 @@ name: cranial motor neuron def: "Motor neuron that innervate muscles that control eye, jaw, and facial movements of the vertebrate head and parasympathetic neurons that innervate certain glands and organs." [ZFIN:CVS] synonym: "cranial motoneuron" EXACT [] xref: PMID:14699587 -xref: ZFA:0005730 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005730 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000100 ! motor neuron [Term] @@ -27863,8 +27891,10 @@ subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0005006 ! ionocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2473-2313 +intersection_of: CL:0005006 ! ionocyte +intersection_of: part_of UBERON:0000115 ! lung epithelium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2473-2313 [Term] id: CL:0017001 @@ -27872,7 +27902,7 @@ name: splanchnic mesodermal cell def: "A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm." [] is_a: CL:0011010 ! lateral mesodermal cell relationship: part_of UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2473-2313 +property_value: terms:contributor https://orcid.org/0000-0003-2473-2313 [Term] id: CL:0017002 @@ -27923,7 +27953,7 @@ xref: EFO:0000572 xref: FMA:83030 is_a: CL:0000542 ! lymphocyte relationship: output_of GO:0046649 ! lymphocyte activation -property_value: http://purl.org/dc/elements/1.1/date "2022-08-17T14:20:01Z" xsd:string +property_value: dc:date "2022-08-17T14:20:01Z" xsd:string created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -27935,7 +27965,7 @@ xref: EFO:0005293 xref: FMA:83031 is_a: CL:0000945 ! lymphocyte of B lineage is_a: CL:0017005 ! lymphoblast -property_value: http://purl.org/dc/elements/1.1/date "2022-08-17T14:30:32Z" xsd:string +property_value: dc:date "2022-08-17T14:30:32Z" xsd:string created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -27946,7 +27976,7 @@ synonym: "AS DC, human" EXACT [] is_a: CL:0001056 ! dendritic cell, human relationship: RO:0002292 PR:O43699 ! expresses sialic acid-binding Ig-like lectin 6 (human) relationship: RO:0002292 PR:P30530 ! expresses tyrosine-protein kinase receptor UFO (human) -property_value: http://purl.org/dc/elements/1.1/date "2022-08-25T14:18:37Z" xsd:dateTime +property_value: dc:date "2022-08-25T14:18:37Z" xsd:dateTime created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -27958,8 +27988,8 @@ is_a: CL:1000296 ! epithelial cell of urethra is_a: CL:4030024 ! hillock cell intersection_of: CL:4030024 ! hillock cell intersection_of: part_of UBERON:0000057 ! urethra -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-2473-2313 -property_value: http://purl.org/dc/terms/date "2022-10-13T13:51:35Z" xsd:dateTime +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-10-13T13:51:35Z" xsd:dateTime [Term] id: CL:0017011 @@ -27971,9 +28001,9 @@ is_a: CL:0017003 ! epithelial cell of prostatic urethra is_a: CL:0017010 ! hillock cell of urethral epithelium intersection_of: CL:4030024 ! hillock cell intersection_of: part_of UBERON:0001335 ! prostatic urethra -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-2473-2313 -property_value: http://purl.org/dc/terms/date "2022-10-13T13:58:15Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0003-2473-2313 +property_value: terms:date "2022-10-13T13:58:15Z" xsd:dateTime [Term] id: CL:0017500 @@ -27983,7 +28013,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -27992,7 +28022,7 @@ name: obsolete lobed nucleus def: "Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin." [GOC:tfm] comment: Obsoleted because duplicate with GO term. relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/734 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true replaced_by: GO:0098537 creation_date: 2009-12-22T03:54:43Z @@ -28006,7 +28036,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -28017,7 +28047,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -28028,7 +28058,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -28037,7 +28067,7 @@ name: obsolete increased nucleus size def: "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [GOC:tfm] comment: This class was a phenotype, not a cell type. relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2251 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true replaced_by: PATO:0040072 creation_date: 2009-12-23T10:53:24Z @@ -28047,7 +28077,7 @@ id: CL:0017506 name: banded nucleus def: "A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament." [GOC:tfm] is_a: GO:0005634 ! nucleus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-23T02:18:43Z [Term] @@ -28058,7 +28088,7 @@ is_a: GO:0005634 ! nucleus intersection_of: GO:0005634 ! nucleus intersection_of: bearer_of PATO:0001871 ! reniform relationship: bearer_of PATO:0001871 ! reniform -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-23T02:31:25Z [Term] @@ -28066,7 +28096,7 @@ id: CL:0017508 name: cartwheel heterochromatin def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:28:35Z [Term] @@ -28089,8 +28119,8 @@ is_a: CL:0000313 ! serous secreting cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-05-07T16:03:27Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-05-07T16:03:27Z" xsd:dateTime [Term] id: CL:0019002 @@ -28103,9 +28133,9 @@ is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-05-07T17:29:51Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-05-07T17:29:51Z" xsd:dateTime [Term] id: CL:0019003 @@ -28118,10 +28148,10 @@ synonym: "goblet cell of tracheobronchial tree" EXACT [] is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002370 ! respiratory goblet cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-05-07T18:14:52Z" xsd:dateTime +intersection_of: part_of UBERON:0008397 ! tracheobronchial epithelium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-05-07T18:14:52Z" xsd:dateTime [Term] id: CL:0019015 @@ -28134,9 +28164,9 @@ is_a: CL:0000774 ! band form eosinophil intersection_of: CL:0000774 ! band form eosinophil intersection_of: part_of UBERON:0008946 ! lung parenchyma relationship: part_of UBERON:0008946 ! lung parenchyma -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-05-26T09:42:19Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-05-26T09:42:19Z" xsd:dateTime [Term] id: CL:0019017 @@ -28148,9 +28178,9 @@ is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001473 ! lymphatic vessel relationship: part_of UBERON:0001473 ! lymphatic vessel -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-07-21T12:29:51Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-07-21T12:29:51Z" xsd:dateTime [Term] id: CL:0019018 @@ -28162,9 +28192,9 @@ is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-07-21T12:42:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-07-21T12:42:48Z" xsd:dateTime [Term] id: CL:0019019 @@ -28177,9 +28207,9 @@ is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree relationship: part_of UBERON:0007196 ! tracheobronchial tree -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-07-21T12:50:22Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-07-21T12:50:22Z" xsd:dateTime [Term] id: CL:0019020 @@ -28190,8 +28220,8 @@ is_a: CL:1000488 ! cholangiocyte intersection_of: CL:1000488 ! cholangiocyte intersection_of: part_of UBERON:0004822 ! extrahepatic bile duct epithelium relationship: part_of UBERON:0004822 ! extrahepatic bile duct epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-09-03T12:24:24Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-09-03T12:24:24Z" xsd:dateTime [Term] id: CL:0019021 @@ -28205,8 +28235,8 @@ is_a: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: adjacent_to UBERON:0001279 ! portal triad relationship: adjacent_to UBERON:0001279 ! portal triad -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-09-09T13:56:47Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-09-09T13:56:47Z" xsd:dateTime [Term] id: CL:0019022 @@ -28220,8 +28250,8 @@ is_a: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: adjacent_to UBERON:0006841 ! central vein of liver relationship: adjacent_to UBERON:0006841 ! central vein of liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-09-10T12:38:29Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-09-10T12:38:29Z" xsd:dateTime [Term] id: CL:0019026 @@ -28234,9 +28264,9 @@ is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte intersection_of: part_of UBERON:8400006 ! liver lobule periportal region relationship: part_of UBERON:8400006 ! liver lobule periportal region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-10-12T10:29:31Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-10-12T10:29:31Z" xsd:dateTime [Term] id: CL:0019028 @@ -28249,9 +28279,9 @@ is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte intersection_of: part_of UBERON:8400007 ! liver lobule centrilobular region relationship: part_of UBERON:8400007 ! liver lobule centrilobular region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-10-12T10:57:40Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-10-12T10:57:40Z" xsd:dateTime [Term] id: CL:0019029 @@ -28264,9 +28294,9 @@ is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte intersection_of: part_of UBERON:8400008 ! liver lobule midzonal region relationship: part_of UBERON:8400008 ! liver lobule midzonal region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-10-12T11:03:51Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-10-12T11:03:51Z" xsd:dateTime [Term] id: CL:0019031 @@ -28278,8 +28308,8 @@ is_a: CL:0000160 ! goblet cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-10-14T14:59:07Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-10-14T14:59:07Z" xsd:dateTime [Term] id: CL:0019032 @@ -28292,9 +28322,9 @@ is_a: CL:0002204 ! brush cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X -property_value: http://purl.org/dc/terms/date "2020-10-15T12:47:46Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:date "2020-10-15T12:47:46Z" xsd:dateTime [Term] id: CL:0700009 @@ -28303,7 +28333,7 @@ def: "OBSOLETE. A renal beta-intercalated cell that is part of the cortical coll comment: Created with IRI in incorrect ID range synonym: "B-IC" EXACT [PMID:32016094] synonym: "kidney collecting duct intercalated cell type B" EXACT [PMID:31300091] -property_value: http://purl.org/dc/terms/date "2022-08-26T10:31:29Z" xsd:dateTime +property_value: terms:date "2022-08-26T10:31:29Z" xsd:dateTime is_obsolete: true replaced_by: CL:4030005 @@ -28357,13 +28387,13 @@ relationship: part_of UBERON:0002240 ! spinal cord [Term] id: CL:1000082 name: stretch receptor cell -xref: ZFA:0009370 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009370 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 ! neuronal receptor cell [Term] id: CL:1000083 name: stratified keratinized epithelial stem cell -xref: ZFA:0009371 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009371 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000357 ! stratified epithelial stem cell [Term] @@ -28394,13 +28424,13 @@ relationship: part_of UBERON:0005146 ! metanephric nephron tubule [Term] id: CL:1000143 name: lung goblet cell -def: "Any goblet cell that is part of some lung." [FBC:Autogenerated] +def: "Any goblet cell that is part of some lung epithelium." [FBC:Autogenerated] subset: cellxgene_subset is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002370 ! respiratory goblet cell is_a: CL:1000272 ! lung secretory cell intersection_of: CL:0000160 ! goblet cell -intersection_of: part_of UBERON:0002048 ! lung +intersection_of: part_of UBERON:0000115 ! lung epithelium [Term] id: CL:1000147 @@ -28408,7 +28438,7 @@ name: cardiac valve cell def: "A cell that is part of a cardiac valve." [PMID:25311230] subset: cellxgene_subset synonym: "heart valve cell" EXACT [PMID:30796046] -xref: ZFA:0009402 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009402 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000946 ! cardiac valve @@ -28419,7 +28449,7 @@ id: CL:1000155 name: Malpighian tubule stellate cell def: "A specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium." [GO:0061330] synonym: "Malpighian tubule Type II cell" EXACT [FBbt:00005797] -xref: FBbt:00005797 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005797 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0001054 ! Malpighian tubule @@ -28471,7 +28501,6 @@ subset: human_reference_atlas synonym: "PNEC" RELATED OMO:0003000 [PMID:33355253] synonym: "pulmonary neuroendocrine cell" EXACT [PMID:33355253] is_a: CL:0000006 ! neuronal receptor cell -is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000165 ! neuroendocrine cell is_a: CL:0000206 ! chemoreceptor cell @@ -29233,6 +29262,7 @@ id: CL:1000347 name: enterocyte of colon def: "A columnar cell of the colon that is part of the colonic epithelium." [GOC:tfm] subset: cellxgene_subset +synonym: "colonocyte" EXACT [PMID:34497389] synonym: "vacuolar absorptive cell of epithelium of colon" NARROW [] xref: FMA:263114 is_a: CL:0002071 {is_inferred="true"} ! enterocyte of epithelium of large intestine @@ -29247,7 +29277,6 @@ def: "A basal cell that is part of the epithelium of trachea." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas xref: FMA:263118 -is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea @@ -29275,8 +29304,6 @@ name: basal cell of epithelium of terminal bronchiole def: "A basal cell that is part of the epithelium of terminal bronchiole." [GOC:tfm] subset: human_reference_atlas xref: FMA:263122 -is_a: CL:0000082 ! epithelial cell of lung -is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001958 ! terminal bronchiole epithelium @@ -29289,8 +29316,6 @@ name: basal cell of epithelium of respiratory bronchiole def: "A basal cell that is part of the epithelium of respiratory bronchiole." [GOC:tfm] subset: human_reference_atlas xref: FMA:263124 -is_a: CL:0000082 ! epithelial cell of lung -is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001955 ! epithelium of respiratory bronchiole @@ -29303,8 +29328,6 @@ name: basal cell of epithelium of lobular bronchiole def: "A basal cell that is part of the epithelium of bronchiole." [GOC:tfm] subset: human_reference_atlas xref: FMA:263126 -is_a: CL:0000082 ! epithelial cell of lung -is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:8600001 ! epithelium of lobular bronchiole @@ -29660,6 +29683,7 @@ synonym: "liver sinusoidal endothelial cell" EXACT [PMID:30348985] synonym: "LSEC" EXACT [PMID:30348985] xref: BTO:000125 xref: FMA:62911 +is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002262 ! endothelial cell of sinusoid intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001281 ! hepatic sinusoid @@ -29717,7 +29741,6 @@ name: endothelial cell of Peyer's patch def: "An endothelial cell that is part of the small intestine Peyer's patch." [GOC:tfm] xref: FMA:67757 is_a: CL:0000115 {is_inferred="true"} ! endothelial cell -is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003454 ! small intestine Peyer's patch relationship: part_of UBERON:0003454 ! small intestine Peyer's patch @@ -29759,7 +29782,7 @@ def: "An endothelial cell that is part of the venule." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas xref: FMA:67762 -is_a: CL:0002139 {is_inferred="true"} ! endothelial cell of vascular tree +is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0001979 ! venule relationship: part_of UBERON:0001979 ! venule @@ -29877,7 +29900,7 @@ def: "A somatic stem cell that is part of the epidermis." [GOC:tfm] subset: cellxgene_subset synonym: "epidermal stem cell" EXACT [FMA:70541] xref: FMA:70541 -xref: ZFA:0007122 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007122 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 {is_inferred="true"} ! somatic stem cell intersection_of: CL:0000723 ! somatic stem cell intersection_of: part_of UBERON:0001003 ! skin epidermis @@ -30336,7 +30359,7 @@ def: "An epithelial cell that is part of the bile duct. Cholangiocytes contribut subset: cellxgene_subset synonym: "epithelial cell of bile duct" EXACT [] xref: FMA:86481 -xref: ZFA:0009397 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009397 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000069 {is_inferred="true"} ! branched duct epithelial cell intersection_of: CL:0000069 ! branched duct epithelial cell @@ -30398,7 +30421,6 @@ def: "A mesothelial cell that is part of the visceral pleura." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas xref: FMA:86739 -is_a: CL:0000082 ! epithelial cell of lung is_a: CL:1000491 ! mesothelial cell of pleura intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002401 ! visceral pleura @@ -30440,7 +30462,7 @@ name: kidney cell def: "A cell that is part of a kidney." [] subset: cellxgene_subset xref: KUPO:0001010 -xref: ZFA:0009389 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002113 ! kidney @@ -30453,7 +30475,7 @@ def: "A cell that is part of kidney interstitium." [] subset: cellxgene_subset subset: kidney_upper_slim xref: KUPO:0001013 -xref: ZFA:0009390 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009390 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell is_a: CL:4030031 ! interstitial cell intersection_of: CL:1000497 ! kidney cell @@ -30465,7 +30487,7 @@ id: CL:1000504 name: kidney medulla cell def: "A cell that is part of a renal medulla." [PMID:22343825] xref: KUPO:0001017 -xref: ZFA:0009391 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009391 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0000362 ! renal medulla @@ -30622,7 +30644,7 @@ name: kidney corpuscule cell def: "Any renal cortical epithelial cell that is part of some renal corpuscle." [FBC:Autogenerated] subset: kidney_upper_slim xref: KUPO:0001021 -is_a: CL:0002584 {is_inferred="true"} ! renal cortical epithelial cell +is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron intersection_of: CL:0002584 ! renal cortical epithelial cell intersection_of: part_of UBERON:0001229 ! renal corpuscle @@ -30924,7 +30946,7 @@ id: CL:1000746 name: glomerular cell def: "Any kidney corpuscule cell that is part of some renal glomerulus." [FBC:Autogenerated] xref: KUPO:0001036 -is_a: CL:1000612 {is_inferred="true"} ! kidney corpuscule cell +is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus @@ -30969,11 +30991,12 @@ relationship: part_of UBERON:0005213 ! outer renal medulla interstitium [Term] id: CL:1000838 name: kidney proximal convoluted tubule epithelial cell -def: "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule." [FBC:Autogenerated] +def: "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border." [FBC:Autogenerated] subset: cellxgene_subset xref: KUPO:0001045 -is_a: CL:0002306 {is_inferred="true"} ! epithelial cell of proximal tubule +is_a: CL:0002307 ! brush border cell of the proximal tubule intersection_of: CL:0002306 ! epithelial cell of proximal tubule +intersection_of: has_part GO:0005903 ! brush border intersection_of: part_of UBERON:0001287 ! proximal convoluted tubule relationship: part_of UBERON:0001287 ! proximal convoluted tubule @@ -31024,7 +31047,6 @@ name: kidney blood vessel cell def: "A blood vessel cell that is part of a kidney." [PMID:34843404] xref: KUPO:0001014 is_a: BFO:0000002 -is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel @@ -31099,8 +31121,7 @@ subset: human_reference_atlas xref: KUPO:0001037 is_a: CL:0002144 ! capillary endothelial cell is_a: CL:0002188 ! glomerular endothelial cell -is_a: CL:1000510 ! kidney glomerular epithelial cell -is_a: CL:1000892 {is_inferred="true"} ! kidney capillary endothelial cell +is_a: CL:1000892 ! kidney capillary endothelial cell intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0004294 ! glomerular capillary endothelium relationship: part_of UBERON:0004294 ! glomerular capillary endothelium @@ -31111,7 +31132,7 @@ id: CL:1001006 name: kidney afferent arteriole cell def: "Any kidney arterial blood vessel cell that is part of some renal afferent arteriole." [FBC:Autogenerated] xref: KUPO:0001038 -is_a: CL:1000612 ! kidney corpuscule cell +is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000891 {is_inferred="true"} ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0004639 ! renal afferent arteriole @@ -31122,8 +31143,8 @@ id: CL:1001009 name: kidney efferent arteriole cell def: "Any kidney arterial blood vessel cell that is part of some renal efferent arteriole." [FBC:Autogenerated] xref: KUPO:0001041 -is_a: CL:1000612 ! kidney corpuscule cell -is_a: CL:1000891 {is_inferred="true"} ! kidney arterial blood vessel cell +is_a: CL:0002681 ! kidney cortical cell +is_a: CL:1000891 ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0004640 ! renal efferent arteriole relationship: part_of UBERON:0004640 ! renal efferent arteriole @@ -31184,7 +31205,8 @@ name: kidney cortex artery cell def: "Any kidney arterial blood vessel cell that is part of some renal cortex artery." [FBC:Autogenerated] subset: cellxgene_subset xref: KUPO:0001077 -is_a: CL:1000891 {is_inferred="true"} ! kidney arterial blood vessel cell +is_a: CL:0002681 ! kidney cortical cell +is_a: CL:1000891 ! kidney arterial blood vessel cell intersection_of: CL:1000891 ! kidney arterial blood vessel cell intersection_of: part_of UBERON:0005268 ! renal cortex artery relationship: part_of UBERON:0005268 ! renal cortex artery @@ -31194,6 +31216,7 @@ id: CL:1001052 name: kidney cortex vein cell def: "Any kidney venous blood vessel cell that is part of some renal cortex vein." [FBC:Autogenerated] xref: KUPO:0001084 +is_a: CL:0002681 ! kidney cortical cell is_a: CL:1000893 {is_inferred="true"} ! kidney venous blood vessel cell intersection_of: CL:1000893 ! kidney venous blood vessel cell intersection_of: part_of UBERON:0005269 ! renal cortex vein @@ -31204,7 +31227,6 @@ id: CL:1001064 name: kidney artery smooth muscle cell comment: Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure. xref: KUPO:0001096 -is_a: CL:0002078 ! meso-epithelial cell is_a: CL:0019018 ! blood vessel smooth muscle cell is_a: CL:1000891 ! kidney arterial blood vessel cell @@ -31213,7 +31235,6 @@ id: CL:1001066 name: kidney arteriole smooth muscle cell comment: Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure. xref: KUPO:0001098 -is_a: CL:0002078 ! meso-epithelial cell is_a: CL:0019018 ! blood vessel smooth muscle cell is_a: CL:1000891 ! kidney arterial blood vessel cell @@ -31222,7 +31243,6 @@ id: CL:1001068 name: kidney venous system smooth muscle cell comment: Note that the source of this term is KUPO:0001068 (venous system smooth muscle cell), which we believe actually denotes the kidney specific structure. xref: KUPO:0001100 -is_a: CL:0002078 ! meso-epithelial cell is_a: CL:0019018 ! blood vessel smooth muscle cell is_a: CL:1000893 ! kidney venous blood vessel cell @@ -31258,7 +31278,7 @@ def: "Any endothelial cell that is part of some renal efferent arteriole." [FBC: subset: cellxgene_subset subset: human_reference_atlas xref: KUPO:0001042 -is_a: CL:1000412 {is_inferred="true"} ! endothelial cell of arteriole +is_a: CL:1000412 ! endothelial cell of arteriole is_a: CL:1001009 ! kidney efferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004640 ! renal efferent arteriole @@ -31361,7 +31381,8 @@ id: CL:1001124 name: kidney cortex peritubular capillary cell def: "Any peritubular capillary endothelial cell that is part of some renal cortex peritubular capillary." [FBC:Autogenerated] xref: KUPO:0001067 -is_a: CL:1001033 {is_inferred="true"} ! peritubular capillary endothelial cell +is_a: CL:0002681 ! kidney cortical cell +is_a: CL:1001033 ! peritubular capillary endothelial cell intersection_of: CL:1001033 ! peritubular capillary endothelial cell intersection_of: part_of UBERON:0006851 ! renal cortex peritubular capillary relationship: part_of UBERON:0006851 ! renal cortex peritubular capillary @@ -31795,8 +31816,8 @@ relationship: part_of UBERON:0001930 ! paraventricular nucleus of hypothalamus id: CL:1001509 name: glycinergic neuron def: "The neurons that utilize glycine as a neurotransmitter." [MP:0010385] -xref: FBbt:00048032 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -xref: ZFA:0009396 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: FBbt:00048032 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: ZFA:0009396 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -31849,7 +31870,6 @@ name: lung endothelial cell def: "Any endothelial cell of vascular tree that is part of some lung." [FBC:Autogenerated] synonym: "endothelial cell of lung" RELATED [] synonym: "pulmonary vessel endothelial cell" RELATED [] -is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0002048 ! lung @@ -31902,7 +31922,6 @@ synonym: "colon endothelial cells" RELATED OMO:0003004 [CALOHA:TS-2397] synonym: "colonic endothelial cell" RELATED [CALOHA:TS-2397] xref: CALOHA:TS-2397 is_a: CL:0000115 ! endothelial cell -is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0013695 ! colon endothelium @@ -32343,7 +32362,7 @@ is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0001003 ! skin epidermis relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-03T23:03:09Z [Term] @@ -32356,7 +32375,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0000178 ! blood relationship: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-11T17:29:04Z [Term] @@ -32384,7 +32403,7 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000007 ! pituitary gland relationship: part_of UBERON:0000007 ! pituitary gland -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-03-26T22:14:56Z [Term] @@ -32395,7 +32414,7 @@ is_a: CL:0000126 ! macroglial cell intersection_of: CL:0000126 ! macroglial cell intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-03-28T21:35:27Z [Term] @@ -32407,7 +32426,7 @@ is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: part_of UBERON:0002372 ! tonsil relationship: part_of UBERON:0002372 ! tonsil -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-03-28T21:35:33Z [Term] @@ -32418,7 +32437,7 @@ is_a: CL:1001607 ! articular chondrocyte intersection_of: CL:1001607 ! articular chondrocyte intersection_of: part_of UBERON:0001485 ! knee joint relationship: part_of UBERON:0001485 ! knee joint -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T14:40:11Z [Term] @@ -32429,14 +32448,14 @@ is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium relationship: part_of UBERON:0008339 ! microvascular endothelium -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:07:42Z [Term] id: CL:2000009 name: obsolete microvascular endothelium blood vessel endothelial cell def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 is_obsolete: true replaced_by: CL:2000008 creation_date: 2014-06-04T15:09:18Z @@ -32449,7 +32468,7 @@ is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:12:06Z [Term] @@ -32460,7 +32479,7 @@ is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0002067 ! dermis -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:15:08Z [Term] @@ -32471,7 +32490,7 @@ is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0003530 ! pedal digit skin relationship: part_of UBERON:0003530 ! pedal digit skin -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:16:44Z [Term] @@ -32482,7 +32501,7 @@ is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001416 ! skin of abdomen relationship: part_of UBERON:0001416 ! skin of abdomen -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:18:16Z [Term] @@ -32493,7 +32512,7 @@ is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0004262 ! upper leg skin relationship: part_of UBERON:0004262 ! upper leg skin -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:19:44Z [Term] @@ -32504,7 +32523,7 @@ is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001460 ! arm relationship: part_of UBERON:0001460 ! arm -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:29:06Z [Term] @@ -32516,7 +32535,7 @@ is_a: CL:1001567 ! lung endothelial cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:1001567 ! lung endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T16:00:56Z [Term] @@ -32527,7 +32546,7 @@ is_a: CL:0002556 ! fibroblast of periodontium intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0008266 ! periodontal ligament relationship: part_of UBERON:0008266 ! periodontal ligament -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T16:50:33Z [Term] @@ -32540,19 +32559,19 @@ is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:1000413 ! endothelial cell of artery intersection_of: part_of UBERON:0001621 ! coronary artery relationship: part_of UBERON:0001621 ! coronary artery -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T17:08:47Z [Term] id: CL:2000019 name: compound eye photoreceptor cell def: "Any photoreceptor cell that is part of a compound eye." [GOC:TermGenie] -xref: FBbt:00006009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00006009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000287 ! eye photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000018 ! compound eye relationship: part_of UBERON:0000018 ! compound eye -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:16:45Z [Term] @@ -32563,7 +32582,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000087 ! inner cell mass relationship: part_of UBERON:0000087 ! inner cell mass -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:16:53Z [Term] @@ -32575,7 +32594,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001821 ! sebaceous gland relationship: part_of UBERON:0001821 ! sebaceous gland -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:17:00Z [Term] @@ -32586,7 +32605,7 @@ is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002099 ! cardiac septum relationship: part_of UBERON:0002099 ! cardiac septum -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:17:07Z [Term] @@ -32597,7 +32616,7 @@ is_a: CL:0005000 ! spinal cord interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0005375 ! has soma location spinal cord ventral column relationship: RO:0002100 UBERON:0005375 ! has soma location spinal cord ventral column -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:23:36Z [Term] @@ -32608,7 +32627,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0004059 ! has soma location spinal cord medial motor column relationship: RO:0002100 UBERON:0004059 ! has soma location spinal cord medial motor column -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:23:43Z [Term] @@ -32619,14 +32638,14 @@ is_a: CL:0000128 ! oligodendrocyte intersection_of: CL:0000128 ! oligodendrocyte intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:23:50Z [Term] id: CL:2000026 name: obsolete cerebellum Golgi cell def: "Any Golgi cell that is part of a cerebellum." [GOC:TermGenie] -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 is_obsolete: true creation_date: 2014-06-25T00:23:57Z @@ -32639,7 +32658,7 @@ is_a: CL:0000402 ! CNS interneuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:24:03Z [Term] @@ -32650,7 +32669,7 @@ is_a: CL:0000679 ! glutamatergic neuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:24:10Z [Term] @@ -32661,7 +32680,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system relationship: RO:0002100 UBERON:0001017 ! has soma location central nervous system -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:43Z [Term] @@ -32672,7 +32691,7 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001898 ! hypothalamus relationship: part_of UBERON:0001898 ! hypothalamus -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:50Z [Term] @@ -32683,7 +32702,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:2000120 ! has soma location lateral line ganglion relationship: RO:0002100 UBERON:2000120 ! has soma location lateral line ganglion -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:57Z [Term] @@ -32700,8 +32719,8 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0000010 ! has soma location peripheral nervous system relationship: RO:0002100 UBERON:0000010 ! has soma location peripheral nervous system -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T02:28:17Z [Term] @@ -32712,7 +32731,7 @@ is_a: CL:0002187 ! basal cell of epidermis intersection_of: CL:0002187 ! basal cell of epidermis intersection_of: part_of UBERON:0002101 ! limb relationship: part_of UBERON:0002101 ! limb -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T02:28:25Z [Term] @@ -32723,7 +32742,7 @@ is_a: CL:0000856 ! neuromast hair cell intersection_of: CL:0000856 ! neuromast hair cell intersection_of: part_of UBERON:2001470 ! anterior lateral line relationship: part_of UBERON:2001470 ! anterior lateral line -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:37Z [Term] @@ -32734,7 +32753,7 @@ is_a: CL:0000851 ! neuromast mantle cell intersection_of: CL:0000851 ! neuromast mantle cell intersection_of: part_of UBERON:2001470 ! anterior lateral line relationship: part_of UBERON:2001470 ! anterior lateral line -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:44Z [Term] @@ -32746,7 +32765,7 @@ is_a: CL:0000852 ! neuromast supporting cell intersection_of: CL:0000852 ! neuromast supporting cell intersection_of: part_of UBERON:2001470 ! anterior lateral line relationship: part_of UBERON:2001470 ! anterior lateral line -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:51Z [Term] @@ -32757,7 +32776,7 @@ is_a: CL:0000856 ! neuromast hair cell intersection_of: CL:0000856 ! neuromast hair cell intersection_of: part_of UBERON:0006334 ! posterior lateral line relationship: part_of UBERON:0006334 ! posterior lateral line -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:57Z [Term] @@ -32768,7 +32787,7 @@ is_a: CL:0000851 ! neuromast mantle cell intersection_of: CL:0000851 ! neuromast mantle cell intersection_of: part_of UBERON:0006334 ! posterior lateral line relationship: part_of UBERON:0006334 ! posterior lateral line -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:45:04Z [Term] @@ -32780,7 +32799,7 @@ is_a: CL:0000852 ! neuromast supporting cell intersection_of: CL:0000852 ! neuromast supporting cell intersection_of: part_of UBERON:0006334 ! posterior lateral line relationship: part_of UBERON:0006334 ! posterior lateral line -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:45:11Z [Term] @@ -32792,8 +32811,8 @@ is_a: CL:1001319 ! bladder cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0001255 ! urinary bladder -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:04:47Z [Term] @@ -32801,11 +32820,11 @@ id: CL:2000041 name: dermis microvascular lymphatic vessel endothelial cell def: "Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] subset: cellxgene_subset +is_a: CL:0011030 ! dermal microvascular endothelial cell is_a: CL:2000011 ! dermis lymphatic vessel endothelial cell intersection_of: CL:2000011 ! dermis lymphatic vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium -relationship: part_of UBERON:0008339 ! microvascular endothelium -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:09:54Z [Term] @@ -32817,7 +32836,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:12:00Z [Term] @@ -32829,7 +32848,7 @@ is_a: CL:0002575 ! central nervous system pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:18:22Z [Term] @@ -32841,7 +32860,7 @@ is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:24:53Z [Term] @@ -32853,8 +32872,8 @@ is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:1000458 ! melanocyte of skin intersection_of: part_of UBERON:0001471 ! skin of prepuce of penis relationship: part_of UBERON:0001471 ! skin of prepuce of penis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0009-0000-8480-9277 -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 creation_date: 2014-07-09T00:45:07Z [Term] @@ -32866,7 +32885,7 @@ is_a: CL:0000746 ! cardiac muscle cell intersection_of: CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-08-12T20:50:28Z [Term] @@ -32878,7 +32897,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000100 ! motor neuron intersection_of: RO:0002100 UBERON:0002298 ! has soma location brainstem relationship: RO:0002100 UBERON:0002298 ! has soma location brainstem -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-02T23:52:53Z [Term] @@ -32892,7 +32911,7 @@ xref: NCIT:C12645 is_a: CL:0008039 ! lower motor neuron is_a: CL:0011001 ! spinal cord motor neuron relationship: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-03T00:26:27Z [Term] @@ -32904,7 +32923,7 @@ is_a: CL:4023111 ! cerebral cortex pyramidal neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T17:39:04Z [Term] @@ -32912,7 +32931,7 @@ id: CL:2000050 name: obsolete retina retinal ganglion cell def: "Any retinal ganglion cell that is part of a retina." [GOC:TermGenie] comment: http://www.ncbi.nlm.nih.gov/pubmed/2889210 -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 is_obsolete: true creation_date: 2014-10-06T17:43:59Z @@ -32924,7 +32943,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T18:58:47Z [Term] @@ -32937,7 +32956,7 @@ is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:1000413 ! endothelial cell of artery intersection_of: part_of UBERON:0002331 ! umbilical cord relationship: part_of UBERON:0002331 ! umbilical cord -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:01:48Z [Term] @@ -32950,8 +32969,8 @@ is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:06:04Z [Term] @@ -32975,7 +32994,7 @@ is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:16:11Z [Term] @@ -32983,7 +33002,7 @@ id: CL:2000056 name: Meynert cell def: "Any pyramidal cell that is part of a regional part of cerebral cortex." [GOC:TermGenie] is_a: CL:2000049 ! primary motor cortex pyramidal cell -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:20:41Z [Term] @@ -32996,7 +33015,7 @@ is_a: CL:0001035 ! bone cell intersection_of: CL:0000062 ! osteoblast intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0000981 ! femur -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:29:45Z [Term] @@ -33008,7 +33027,7 @@ is_a: CL:0000062 ! osteoblast intersection_of: CL:0000062 ! osteoblast intersection_of: part_of UBERON:0003129 ! skull relationship: part_of UBERON:0003129 ! skull -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:48:30Z [Term] @@ -33021,7 +33040,7 @@ is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:46:27Z [Term] @@ -33038,8 +33057,8 @@ is_a: CL:0000351 ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: part_of UBERON:0010005 ! placental labyrinth villous relationship: part_of UBERON:0010005 ! placental labyrinth villous -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: seeAlso "http://www.sciencellonline.com/site/productInformation.php?keyword=7120" xsd:string +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:48:27Z [Term] @@ -33052,8 +33071,8 @@ is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:51:11Z [Term] @@ -33067,8 +33086,8 @@ is_a: CL:0009092 ! endothelial cell of placenta intersection_of: CL:0002144 ! capillary endothelial cell intersection_of: part_of UBERON:0010005 ! placental labyrinth villous relationship: part_of UBERON:0010005 ! placental labyrinth villous -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:55:56Z [Term] @@ -33080,7 +33099,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:57:42Z [Term] @@ -33093,7 +33112,7 @@ is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:59:13Z [Term] @@ -33101,12 +33120,12 @@ id: CL:2000065 name: ovarian microvascular endothelial cell def: "Any microvascular endothelial cell that is part of a female urethra." [GOC:TermGenie] comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7300 -is_a: CL:1000296 ! epithelial cell of urethra +is_a: CL:1001320 ! urethra cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0001334 ! female urethra relationship: part_of UBERON:0001334 ! female urethra -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:18:01Z [Term] @@ -33119,8 +33138,8 @@ is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:35:38Z [Term] @@ -33133,8 +33152,8 @@ is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:36:54Z [Term] @@ -33146,7 +33165,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002407 ! pericardium relationship: part_of UBERON:0002407 ! pericardium -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:38:06Z [Term] @@ -33158,7 +33177,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 ! gallbladder -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:41:43Z [Term] @@ -33170,7 +33189,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001776 ! optic choroid -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:50:43Z [Term] @@ -33182,7 +33201,7 @@ is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0000310 ! breast relationship: part_of UBERON:0000310 ! breast -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T19:55:30Z [Term] @@ -33195,7 +33214,7 @@ is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: part_of UBERON:0001013 ! adipose tissue -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T22:13:45Z [Term] @@ -33207,7 +33226,7 @@ is_a: CL:0000333 ! migratory neural crest cell intersection_of: CL:0000333 ! migratory neural crest cell intersection_of: part_of UBERON:0000095 ! cardiac neural crest relationship: part_of UBERON:0000095 ! cardiac neural crest -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-11-05T01:18:43Z [Term] @@ -33219,7 +33238,7 @@ is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-11-05T01:26:50Z [Term] @@ -33230,7 +33249,7 @@ is_a: CL:0000223 ! endodermal cell intersection_of: CL:0000223 ! endodermal cell intersection_of: part_of UBERON:0004044 ! anterior visceral endoderm relationship: part_of UBERON:0004044 ! anterior visceral endoderm -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-11-05T01:34:13Z [Term] @@ -33241,7 +33260,7 @@ is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0002543 ! vein endothelial cell intersection_of: part_of UBERON:0000376 ! hindlimb stylopod relationship: part_of UBERON:0000376 ! hindlimb stylopod -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T18:40:47Z [Term] @@ -33253,7 +33272,7 @@ is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000737 ! striated muscle cell intersection_of: part_of UBERON:0004510 ! skeletal muscle tissue of pectoralis major relationship: part_of UBERON:0004510 ! skeletal muscle tissue of pectoralis major -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T18:48:17Z [Term] @@ -33264,7 +33283,7 @@ is_a: CL:0000669 ! pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T18:51:03Z [Term] @@ -33275,7 +33294,7 @@ is_a: CL:0002540 ! mesenchymal stem cell of the bone marrow intersection_of: CL:0002540 ! mesenchymal stem cell of the bone marrow intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0000981 ! femur -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:07:31Z [Term] @@ -33287,7 +33306,7 @@ is_a: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:34Z [Term] @@ -33298,7 +33317,7 @@ is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:1000458 ! melanocyte of skin intersection_of: part_of UBERON:1000021 ! skin of face relationship: part_of UBERON:1000021 ! skin of face -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:40Z [Term] @@ -33307,7 +33326,7 @@ name: obsolete melanocyte of foreskin def: "OBSOLETE. Any melanocyte of skin that is part of a skin of prepuce of penis." [GOC:TermGenie] comment: Term was merged into foreskin melanocyte CL_2000045 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1562 -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 is_obsolete: true replaced_by: CL:2000045 creation_date: 2014-12-02T19:10:45Z @@ -33320,7 +33339,7 @@ is_a: CL:0000346 ! hair follicle dermal papilla cell intersection_of: CL:0000346 ! hair follicle dermal papilla cell intersection_of: part_of UBERON:0000403 ! scalp relationship: part_of UBERON:0000403 ! scalp -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:50Z [Term] @@ -33331,7 +33350,7 @@ is_a: CL:0000160 ! goblet cell is_a: CL:1000432 ! conjunctival epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001811 ! conjunctiva -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:28:38Z [Term] @@ -33343,7 +33362,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0002331 ! umbilical cord relationship: part_of UBERON:0002331 ! umbilical cord -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T20:14:16Z [Term] @@ -33355,7 +33374,7 @@ is_a: CL:0010011 ! cerebral cortex GABAergic interneuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: RO:0002100 UBERON:0001950 ! has soma location neocortex -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-24T00:37:19Z [Term] @@ -33368,7 +33387,7 @@ is_a: CL:1001569 ! hippocampal interneuron is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-24T00:37:24Z [Term] @@ -33381,7 +33400,7 @@ is_a: CL:1001569 ! hippocampal interneuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn relationship: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-24T00:37:30Z [Term] @@ -33395,7 +33414,7 @@ is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0001033 ! hippocampal granule cell intersection_of: RO:0002100 UBERON:0005381 ! has soma location dentate gyrus granule cell layer relationship: RO:0002100 UBERON:0005381 ! has soma location dentate gyrus granule cell layer -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-02-23T05:48:23Z [Term] @@ -33407,7 +33426,7 @@ is_a: CL:0012001 ! neuron of the forebrain is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0000122 ! stellate neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-02-23T05:48:40Z [Term] @@ -33420,8 +33439,8 @@ is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0015172 ! endometrial blood vessel relationship: part_of UBERON:0015172 ! endometrial blood vessel -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T21:02:36Z [Term] @@ -33433,7 +33452,7 @@ is_a: CL:0000312 ! keratinocyte is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000312 ! keratinocyte intersection_of: part_of UBERON:0002073 ! hair follicle -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T21:07:02Z [Term] @@ -33445,18 +33464,19 @@ is_a: CL:0002553 ! fibroblast of lung intersection_of: CL:0002553 ! fibroblast of lung intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T21:16:22Z [Term] id: CL:2000094 name: nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa def: "Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium." [GOC:TermGenie] +is_a: CL:0002631 ! epithelial cell of upper respiratory tract is_a: CL:1000441 ! epithelial cell of viscerocranial mucosa intersection_of: CL:1000441 ! epithelial cell of viscerocranial mucosa intersection_of: part_of UBERON:0005385 ! nasal cavity respiratory epithelium relationship: part_of UBERON:0005385 ! nasal cavity respiratory epithelium -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T22:25:17Z [Term] @@ -33469,7 +33489,7 @@ is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0012168 ! umbilical cord blood relationship: part_of UBERON:0012168 ! umbilical cord blood -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-05-26T18:58:34Z [Term] @@ -33480,7 +33500,7 @@ is_a: CL:0002551 ! fibroblast of dermis intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001993 ! reticular layer of dermis relationship: part_of UBERON:0001993 ! reticular layer of dermis -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-08-11T16:28:16Z [Term] @@ -33492,7 +33512,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000700 ! dopaminergic neuron intersection_of: RO:0002100 UBERON:0001891 ! has soma location midbrain relationship: RO:0002100 UBERON:0001891 ! has soma location midbrain -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2015-12-03T16:42:40Z [Term] @@ -33504,7 +33524,7 @@ is_a: CL:0002252 ! epithelial cell of esophagus intersection_of: CL:0000067 ! ciliated epithelial cell intersection_of: part_of UBERON:0001976 ! epithelium of esophagus relationship: part_of UBERON:0001976 ! epithelium of esophagus -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 +property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-09T16:40:30Z [Term] @@ -33517,9 +33537,9 @@ subset: human_reference_atlas synonym: "HBC" RELATED OMO:0003000 [] is_a: CL:0000864 ! tissue-resident macrophage relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 creation_date: 2019-02-18T19:41:20Z [Term] @@ -33531,8 +33551,8 @@ is_a: CL:0008025 ! noradrenergic neuron is_a: CL:0011103 ! sympathetic neuron intersection_of: CL:0011103 ! sympathetic neuron intersection_of: capable_of GO:0061533 ! norepinephrine secretion, neurotransmission -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-25T19:30:14Z [Term] @@ -33543,7 +33563,7 @@ is_a: CL:0000108 ! cholinergic neuron is_a: CL:0011103 ! sympathetic neuron intersection_of: CL:0011103 ! sympathetic neuron intersection_of: capable_of GO:0014055 ! acetylcholine secretion, neurotransmission -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 +property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-25T19:32:20Z [Term] @@ -33554,7 +33574,7 @@ is_a: CL:0000101 ! sensory neuron is_a: CL:2000032 ! peripheral nervous system neuron intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 +property_value: terms:contributor http://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-25T19:34:33Z [Term] @@ -33567,7 +33587,7 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000310 ! breast relationship: part_of UBERON:0000310 ! breast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: CL:4006001 @@ -33578,7 +33598,7 @@ is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:8300000 ! skin of scalp relationship: part_of UBERON:8300000 ! skin of scalp -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: CL:4023000 @@ -33587,35 +33607,35 @@ def: "A motor neuron that innervates both intrafusal and extrafusal muscle fiber is_a: CL:0008039 ! lower motor neuron relationship: RO:0002120 CL:0008046 ! synapsed to extrafusal muscle fiber relationship: RO:0002120 CL:0008047 ! synapsed to intrafusal muscle fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023001 name: static beta motor neuron def: "A beta motor neuron that innervates nuclear chain fibers." [PMID:25346659] is_a: CL:4023000 ! beta motor neuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023002 name: dynamic beta motor neuron def: "A beta motor neuron that innervates the nuclear bag fibers of muscle spindles." [PMID:25346659] is_a: CL:4023000 ! beta motor neuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023003 name: nuclear chain fiber def: "A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers." [DOI:10.1016/B978-0-323-39632-5.00024-4, PMID:139469] is_a: CL:0008047 ! intrafusal muscle fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023004 name: nuclear bag fiber def: "A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers." [DOI:10.1016/B978-0-323-39632-5.00024-4, PMID:139469] is_a: CL:0008047 ! intrafusal muscle fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023005 @@ -33624,7 +33644,7 @@ def: "A nuclear bag fiber that is sensitive mainly to the rate of change in musc synonym: "bag1 fiber" EXACT [] synonym: "nuclear bag1 intrafusal fiber" EXACT [] is_a: CL:4023004 ! nuclear bag fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023006 @@ -33633,7 +33653,7 @@ def: "A nuclear bag fiber that is sensitive only changes in muscle length but no synonym: "bag2 fiber" EXACT [] synonym: "nuclear bag2 intrafusal fiber" EXACT [] is_a: CL:4023004 ! nuclear bag fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023007 @@ -33646,8 +33666,8 @@ is_a: CL:4023016 ! vip GABAergic cortical interneuron relationship: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3 bipolar vip interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023008 @@ -33663,9 +33683,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070034 ! intratelencephalic projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070034 ! intratelencephalic projecting -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "IT neuron" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023009 @@ -33681,9 +33701,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070028 ! extratelencephalic projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070028 ! extratelencephalic projecting -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "ET glut" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023010 @@ -33696,8 +33716,8 @@ is_a: BFO:0000002 is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:000005460 ! expresses neuronal acetylcholine receptor subunit alpha-7 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "A7 interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023011 @@ -33706,15 +33726,14 @@ def: "A GABAergic neuron located in the cerebral cortex that expresses Lamp5" [P subset: BDS_subset subset: cellxgene_subset xref: ILX:0770149 -is_a: BFO:0000002 -is_a: CL:0010011 ! cerebral cortex GABAergic interneuron +is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000032148 ! expresses lysosome-associated membrane glycoprotein 5 relationship: RO:0002292 PR:000032148 ! expresses lysosome-associated membrane glycoprotein 5 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "Lamp5 cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023012 @@ -33731,9 +33750,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070030 ! near projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070030 ! near projecting -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "NP glut neuron" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023013 @@ -33749,9 +33768,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070029 ! corticothalamic projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070029 ! corticothalamic projecting -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CT glut" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023014 @@ -33763,8 +33782,8 @@ is_a: CL:4023016 ! vip GABAergic cortical interneuron relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 vip interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023015 @@ -33773,15 +33792,14 @@ def: "A GABAergic neuron located in the cerebral cortex that expresses Gamma-syn subset: BDS_subset subset: cellxgene_subset xref: ILX:0770150 -is_a: BFO:0000002 -is_a: CL:0010011 ! cerebral cortex GABAergic interneuron +is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015325 ! expresses gamma-synuclein relationship: RO:0002292 PR:000015325 ! expresses gamma-synuclein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "sncg cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023016 @@ -33790,15 +33808,14 @@ def: "A GABAergic neuron located in the cerebral cortex that expresses vasoactiv subset: BDS_subset subset: cellxgene_subset xref: ILX:0770151 -is_a: BFO:0000002 -is_a: CL:0010011 ! cerebral cortex GABAergic interneuron +is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000017299 ! expresses VIP peptides relationship: RO:0002292 PR:000017299 ! expresses VIP peptides -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "vip cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023017 @@ -33814,8 +33831,8 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015665 ! expresses somatostatin relationship: RO:0002292 PR:000015665 ! expresses somatostatin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "sst cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023018 @@ -33831,8 +33848,8 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000013502 ! expresses parvalbumin alpha relationship: RO:0002292 PR:000013502 ! expresses parvalbumin alpha -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "pvalb cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023019 @@ -33845,7 +33862,7 @@ is_a: CL:4023071 ! L5/6 cck GABAergic interneuron (Mmus) intersection_of: CL:4023071 ! L5/6 cck GABAergic interneuron (Mmus) intersection_of: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) relationship: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023020 @@ -33853,7 +33870,7 @@ name: dynamic gamma motor neuron def: "A gamma motor neuron that innervates dynamic nuclear bag fibers (bag1 fibers) and enhances the sensitivities of Ia sensory neurons. They alter muscle spindle sensitivity and increases its discharge in response to velocity of muscle length (rather than just magnitude)." [PMID:13933877, PMID:139469, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] is_a: CL:0008037 ! gamma motor neuron relationship: RO:0002120 CL:4023005 ! synapsed to dynamic nuclear bag fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023021 @@ -33861,7 +33878,7 @@ name: static gamma motor neuron def: "A gamma motor neuron that innervates static nuclear bag fibers (bag2 fibers) and increases their firing, in response to an increase in the magnitude of change in length, and controls the static sensitivity of the stretch reflex." [PMID:13933877, PMID:139469, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] is_a: CL:0008037 ! gamma motor neuron relationship: RO:0002120 CL:4023006 ! synapsed to static nuclear bag fiber -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023022 @@ -33871,8 +33888,8 @@ subset: BDS_subset is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "canopy lamp5 interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023023 @@ -33884,8 +33901,8 @@ is_a: CL:0000693 ! neurogliaform cell is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5,6 NGC Lamp5 interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023024 @@ -33897,8 +33914,8 @@ is_a: CL:0000693 ! neurogliaform cell is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "NGC Lamp5 interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023025 @@ -33909,7 +33926,7 @@ synonym: "LP SST (Mus musculus)" EXACT [] is_a: CL:4023121 ! sst chodl GABAergic cortical interneuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023026 @@ -33921,7 +33938,7 @@ synonym: "dSPN" EXACT OMO:0003000 [PMID:30096299] is_a: BFO:0000002 is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023027 @@ -33934,8 +33951,8 @@ is_a: CL:4023086 ! T Martinotti neuron relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 T Martinotti sst interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023028 @@ -33947,8 +33964,8 @@ is_a: CL:4023017 ! sst GABAergic cortical interneuron relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 non-Martinotti sst interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023029 @@ -33960,7 +33977,7 @@ synonym: "iSPN" EXACT OMO:0003000 [PMID:30096299] is_a: BFO:0000002 is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023030 @@ -33973,8 +33990,8 @@ is_a: CL:4023017 ! sst GABAergic cortical interneuron is_a: CL:4023087 ! fan Martinotti neuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3/5 fan Martinotti sst interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023031 @@ -33987,8 +34004,8 @@ is_a: CL:4023076 ! Martinotti neuron relationship: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L4 sst interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023032 @@ -33996,7 +34013,7 @@ name: ON retinal ganglion cell comment: A retinal ganglion cell that is depolarized by illumination of its receptive field center. {xref="PMID:19602302"} subset: cellxgene_subset is_a: CL:0000740 ! retinal ganglion cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023033 @@ -34004,7 +34021,7 @@ name: OFF retinal ganglion cell def: "A retinal ganglion cell that is depolarized by decreased illumination of their receptive field center." [PMID:19602302] subset: cellxgene_subset is_a: CL:0000740 ! retinal ganglion cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023034 @@ -34013,7 +34030,7 @@ def: "OBSOLETE A sst GABAergic cortical interneuron transcriptomically between t comment: Moved to PCL. Use PCL:1000002 instead. synonym: "L2/3 PV-like SST Mus)" EXACT [] relationship: term_tracker_item https://github.com/obophenotype/brain_data_standards_ontologies/issues/231 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: PCL:1000002 @@ -34027,8 +34044,8 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002202 UBERON:0004025 ! develops from lateral ganglionic eminence relationship: RO:0002202 UBERON:0004025 ! develops from lateral ganglionic eminence -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-7073-9172" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0002-7073-9172" xsd:string [Term] id: CL:4023036 @@ -34041,8 +34058,8 @@ synonym: "Chandelier PV" EXACT [] xref: ILX:0107356 is_a: CL:4023018 ! pvalb GABAergic cortical interneuron is_a: CL:4023083 ! chandelier cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "chandelier PV interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023038 @@ -34056,8 +34073,8 @@ is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: RO:0002100 UBERON:8440003 ! has soma location cortical layer VIb relationship: RO:0002100 UBERON:8440003 ! has soma location cortical layer VIb -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6b glut" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023039 @@ -34071,8 +34088,8 @@ intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001876 ! has soma location amygdala relationship: RO:0002100 UBERON:0001876 ! has soma location amygdala -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023040 @@ -34082,8 +34099,8 @@ subset: BDS_subset subset: cellxgene_subset synonym: "L2/3-6 IT projecting neuron" EXACT [] is_a: CL:4023008 ! intratelencephalic-projecting glutamatergic cortical neuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3-6 IT glut" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023041 @@ -34102,8 +34119,8 @@ is_a: CL:4023111 ! cerebral cortex pyramidal neuron intersection_of: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 ET glut" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023042 @@ -34117,8 +34134,8 @@ intersection_of: CL:4023013 ! corticothalamic-projecting glutamatergic cortical intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0013001 UBERON:0010225 ! has synaptic IO in region thalamic complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6 CT glut" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023043 @@ -34133,8 +34150,8 @@ is_a: CL:4030067 ! L5/6 near-projecting glutamatergic neuron intersection_of: CL:4030067 ! L5/6 near-projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5/6 NP glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023044 @@ -34145,8 +34162,8 @@ synonym: "non-MY ET M1" EXACT [] synonym: "non-MY ET MOp (Mus)" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "non-MY ET glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023045 @@ -34160,8 +34177,8 @@ is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070031 ! corticomedulla projecting relationship: RO:0013001 UBERON:0001896 ! has synaptic IO in region medulla oblongata -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "MY ET glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023046 @@ -34171,8 +34188,8 @@ subset: BDS_subset synonym: "L6b subplate glutamatergic neuron of the primary motor cortex" EXACT [] is_a: CL:4023038 ! L6b glutamatergic cortical neuron relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6b subplate glut" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023047 @@ -34186,8 +34203,8 @@ is_a: CL:4030059 ! L2/3 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030059 ! L2/3 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3 IT glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023048 @@ -34202,8 +34219,8 @@ is_a: CL:4030062 ! L4/5 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030062 ! L4/5 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L4/5 IT glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023049 @@ -34217,8 +34234,8 @@ is_a: CL:4030064 ! L5 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030064 ! L5 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 IT glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023050 @@ -34234,8 +34251,8 @@ is_a: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6 IT glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023051 @@ -34247,7 +34264,7 @@ synonym: "VLMC" EXACT [] xref: ILX:0770143 is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx relationship: RO:0002202 CL:0011012 ! develops from neural crest cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023052 @@ -34255,8 +34272,8 @@ name: Betz upper motor neuron def: "A Betz cell that synapses with lower motor neurons directly." [DOI:10.1101/2020.03.31.016972, PMID:18558853, PMID:28751609] is_a: CL:0008049 ! Betz cell relationship: RO:0002120 CL:0008039 ! synapsed to lower motor neuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023053 @@ -34264,9 +34281,9 @@ name: spinal interneuron synapsing Betz cell def: "A Betz cell that syanpses with spinal interneurons." [DOI:10.1101/2020.03.31.016972, PMID:18558853] is_a: CL:0008049 ! Betz cell relationship: RO:0002120 CL:0005000 ! synapsed to spinal cord interneuron -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9685 property_value: RO:0002175 NCBITaxon:9989 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023054 @@ -34275,7 +34292,7 @@ def: "A mesothelial cell that has undergone mesothelial-to-mesenchymal transitio subset: cellxgene_subset is_a: CL:0000057 ! fibroblast relationship: RO:0002202 CL:0000077 ! develops from mesothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023055 @@ -34288,8 +34305,8 @@ synonym: "CT VAL/VM MOp" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023042 ! L6 corticothalamic-projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CT VAL/VM glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023056 @@ -34303,7 +34320,7 @@ relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P11087 {xref="PMID:30096314"} ! expresses collagen alpha-1(I) chain (mouse) relationship: RO:0002292 PR:P26618 {xref="PMID:30096314"} ! expresses platelet-derived growth factor receptor alpha (mouse) relationship: RO:0002292 PR:P51885 {xref="PMID:30096314"} ! expresses lumican (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023057 @@ -34317,8 +34334,8 @@ is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0011005 ! GABAergic interneuron intersection_of: RO:0002100 UBERON:0002129 ! has soma location cerebellar cortex relationship: RO:0002100 UBERON:0002129 ! has soma location cerebellar cortex -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023058 @@ -34329,7 +34346,7 @@ is_a: CL:4023054 ! mesothelial fibroblast intersection_of: CL:4023054 ! mesothelial fibroblast intersection_of: part_of UBERON:0000391 ! leptomeninx relationship: part_of UBERON:0000391 ! leptomeninx -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023059 @@ -34342,8 +34359,8 @@ synonym: "committed oligodendrocyte precursor" EXACT [] synonym: "COP" EXACT OMO:0003000 [] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) relationship: RO:0002202 CL:0002453 ! develops from oligodendrocyte precursor cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023060 @@ -34352,9 +34369,9 @@ def: "A neuron that has its soma located in CA1-3 of the hippocampus." [DOI:10.1 subset: human_reference_atlas is_a: CL:0002608 ! hippocampal neuron relationship: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: IAO:0000116 "It is unclear as to if the modelling of Ammon's horn includes CA4 (which could be considered part of the dentate gyrus) in Uberon, hence no equivalent class axiom was made." xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023061 @@ -34362,8 +34379,8 @@ name: hippocampal CA4 neuron def: "A neuron that has its soma located in CA4 of the hippocampus." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas is_a: CL:0000540 ! neuron -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023062 @@ -34374,8 +34391,8 @@ is_a: CL:0002608 ! hippocampal neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation relationship: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023063 @@ -34388,24 +34405,30 @@ is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002202 UBERON:0004024 ! develops from medial ganglionic eminence relationship: RO:0002202 UBERON:0004024 ! develops from medial ganglionic eminence -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "MGE interneuron" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023064 name: caudal ganglionic eminence derived interneuron -def: "An interneuron that is derived from the caudal ganglionic eminence." [DOI:10.1101/2022.10.12.511898] -subset: human_reference_atlas -synonym: "CGE interneuron" EXACT [] +def: "An interneuron that is derived from the caudal ganglionic eminence." [PMID:20130169, PMID:37824655, PMID:37824663] +subset: human_reference_atlas +synonym: "caudal ganglionic eminence derived GABAergic cortical interneuron" EXACT [PMID:20130169] +synonym: "CGE cortical interneuron" RELATED OMO:0003000 [PMID:20130169] +synonym: "CGE interneuron" EXACT OMO:0003000 [PMID:37824663] +synonym: "CGE interneuron" RELATED OMO:0003000 [PMID:37824663] +synonym: "CGE-derived cell" RELATED OMO:0003000 [PMID:27034423] +synonym: "CGE-derived GABAergic IN" RELATED OMO:0003000 [PMID:27034423] +synonym: "CGE-derived interneuron" RELATED OMO:0003000 [PMID:20130169, PMID:37824655] is_a: BFO:0000002 -is_a: CL:0000099 ! interneuron +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence relationship: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CGE interneuron" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023065 @@ -34417,8 +34440,8 @@ is_a: BFO:0000002 is_a: CL:0000617 ! GABAergic neuron is_a: CL:0010012 ! cerebral cortex neuron relationship: RO:0002292 PR:000010317 ! expresses homeobox protein Meis2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "meis2 GABA" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023066 @@ -34430,7 +34453,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070016 ! horizontal pyramidal morphology relationship: bearer_of PATO:0070016 ! horizontal pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023067 @@ -34439,7 +34462,7 @@ def: "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculu comment: Moved to PCL. Use PCL:1000004 instead. synonym: "Martinotti L2/3 PV-like SST (Mus)" EXACT [] relationship: term_tracker_item https://github.com/obophenotype/brain_data_standards_ontologies/issues/231 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: PCL:1000004 @@ -34454,8 +34477,8 @@ intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission intersection_of: RO:0002100 UBERON:0010225 ! has soma location thalamic complex relationship: RO:0002100 UBERON:0010225 ! has soma location thalamic complex -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023069 @@ -34468,23 +34491,21 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002202 UBERON:0004024 ! develops from medial ganglionic eminence -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "MGE cortical gaba interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023070 -name: caudal ganglionic eminence derived GABAergic cortical interneuron -def: "A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex." [PMID:20130169] +name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron +def: "OBSOLETE. A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex." [PMID:20130169] +comment: caudal ganglionic eminence derived GABAergic interneuron\nand caudal ganglionic eminence derived interneuron are the same cell type. \nThe two must be merged and one needs to be defined as obsolete. \nWe decided to deprecate the entity with the more specific term and redundant qualities \nin the label. See comments in issue 2357. subset: cellxgene_subset synonym: "CGE cortical interneuron" EXACT [] -is_a: CL:0010011 ! cerebral cortex GABAergic interneuron -is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron -intersection_of: CL:0000099 ! interneuron -intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -intersection_of: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/pull/2374 property_value: IAO:0000028 "CGE gaba cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +is_obsolete: true +replaced_by: CL:4023064 [Term] id: CL:4023071 @@ -34497,8 +34518,8 @@ is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P09240 ! expresses cholecystokinin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5/6 cck interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023072 @@ -34509,15 +34530,15 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0008998 ! vasculature of brain relationship: part_of UBERON:0008998 ! vasculature of brain -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023073 name: obsolete choroid plexus cell def: "OBSOLETE. A cell that is part of the choroid plexus." [DOI:10.1101/2022.10.12.511898] relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2043 -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:0000706 @@ -34530,8 +34551,8 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002206 ! has soma location mammillary body relationship: RO:0002100 UBERON:0002206 ! has soma location mammillary body -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023075 @@ -34545,8 +34566,8 @@ relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P24529 ! expresses tyrosine 3-monooxygenase (mouse) relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6 th sst interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023076 @@ -34561,7 +34582,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070007 ! Martinotti morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070007 ! Martinotti morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023077 @@ -34573,7 +34594,7 @@ is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070012 ! bitufted cell morphology relationship: bearer_of PATO:0070012 ! bitufted cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023078 @@ -34582,7 +34603,7 @@ def: "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculu comment: Moved to PCL. Use PCL:1000003 instead. synonym: "basket L2/3 PV-like SST (Mus)" EXACT [] relationship: term_tracker_item https://github.com/obophenotype/brain_data_standards_ontologies/issues/231 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: PCL:1000003 @@ -34596,8 +34617,8 @@ is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: CL:0000540 ! neuron intersection_of: RO:0002202 UBERON:0001891 ! develops from midbrain relationship: RO:0002202 UBERON:0001891 ! develops from midbrain -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023080 @@ -34607,8 +34628,8 @@ subset: BDS_subset synonym: "stellate L6 IT MOp (Mus musculus)" EXACT [] is_a: CL:4023050 ! L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex relationship: bearer_of PATO:0070020 ! stellate pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "stellate L6 IT glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023081 @@ -34618,8 +34639,8 @@ subset: BDS_subset synonym: "inverted L6 IT MOp (Mus musculus)" EXACT [] is_a: CL:4023050 ! L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex relationship: bearer_of PATO:0070021 ! inverted pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "inverted L6 IT glut MOp" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023083 @@ -34633,7 +34654,7 @@ is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0011005 ! GABAergic interneuron intersection_of: bearer_of PATO:0070011 ! chandelier cell morphology relationship: bearer_of PATO:0070011 ! chandelier cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023086 @@ -34646,7 +34667,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070008 ! T Martinotti morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070008 ! T Martinotti morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023087 @@ -34659,7 +34680,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070009 ! fan Martinotti morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070009 ! fan Martinotti morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023088 @@ -34672,7 +34693,7 @@ intersection_of: bearer_of PATO:0070004 ! large basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: bearer_of PATO:0070004 ! large basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023089 @@ -34685,7 +34706,7 @@ intersection_of: bearer_of PATO:0070005 ! nest basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: bearer_of PATO:0070005 ! nest basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023090 @@ -34698,7 +34719,7 @@ intersection_of: bearer_of PATO:0070003 ! small basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: bearer_of PATO:0070003 ! small basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023092 @@ -34710,7 +34731,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070021 ! inverted pyramidal morphology relationship: bearer_of PATO:0070021 ! inverted pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023093 @@ -34722,7 +34743,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070020 ! stellate pyramidal morphology relationship: bearer_of PATO:0070020 ! stellate pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023094 @@ -34734,7 +34755,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070018 ! tufted pyramidal morphology relationship: bearer_of PATO:0070018 ! tufted pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023095 @@ -34746,7 +34767,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070019 ! untufted pyramidal morphology relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023097 @@ -34756,7 +34777,7 @@ synonym: "AB cell" RELATED OMO:0003000 [PMID:23298861] synonym: "ABC" RELATED OMO:0003000 [PMID:30096314] is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx relationship: part_of UBERON:0000437 ! arachnoid barrier layer -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023098 @@ -34764,7 +34785,7 @@ name: obsolete L2/3 intratelencephalic projecting glutamatergic neuron of the pr def: "OBSOLETE An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the human primary motor cortex." [DOI:10.1101/2020.03.31.016972] comment: Made terms species agnostic, use CL:4023047 instead. synonym: "L2/3 IT MOp (human)" EXACT [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023047 @@ -34775,7 +34796,7 @@ def: "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a som comment: Made terms species agnostic, use CL:4023049 instead. synonym: "L5 IT MOp (human)" EXACT [] xref: ILX:0770157 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023049 @@ -34786,7 +34807,7 @@ def: "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a som comment: Made terms species agnostic, use CL:4023050 instead. synonym: "L6 IT MOp (human)" EXACT [] xref: ILX:0770158 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023050 @@ -34797,7 +34818,7 @@ def: "OBSOLETE. A near-projecting glutamatergic neuron with a soma found in laye comment: Made terms species agnostic, use CL:4023043 instead. synonym: "L5/6 NP MOp (human)" EXACT [] xref: ILX:0770161 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023043 @@ -34808,7 +34829,7 @@ def: "OBSOLETE. A near-projecting glutamatergic neuron with a soma found in laye comment: Made terms species agnostic, use CL:4023043 instead. synonym: "L5/6 NP MOp (marmoset)" EXACT [] xref: ILX:0770161 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023043 @@ -34818,7 +34839,7 @@ name: obsolete L2/3 intratelencephalic projecting glutamatergic neuron of the pr def: "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the marmoset primary motor cortex." [DOI:10.1101/2020.03.31.016972] comment: Made terms species agnostic, use CL:4023047 instead. synonym: "L2/3 IT MOp (marmoset)" EXACT [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023047 @@ -34829,7 +34850,7 @@ def: "OBSOLETE An intratelencephalic-projecting glutamatergic neuron with a soma comment: Made terms species agnostic, use CL:4023049 instead. synonym: "L5 IT MOp (marmoset)" EXACT [] xref: ILX:0770157 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023049 @@ -34841,7 +34862,7 @@ comment: Made terms species agnostic, use CL:4023050 instead. subset: BDS_subset synonym: "L6 IT MOp (marmoset)" EXACT [] xref: ILX:0770158 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023050 @@ -34851,7 +34872,7 @@ name: obsolete meis2 expressing cortical GABAergic cell (Callithrix jacchus) def: "OBSOLETE. A mouse GABAergic cell located in the marmoset cerebral cortex that expresses meis2." [DOI:10.1101/2020.03.31.016972] comment: false synonym: "Meis2 (Marmoset)" EXACT [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023065 @@ -34866,7 +34887,7 @@ intersection_of: RO:0002100 UBERON:0002275 ! has soma location reticular formati intersection_of: RO:0013001 UBERON:0002240 ! has synaptic IO in region spinal cord relationship: RO:0002100 UBERON:0002275 ! has soma location reticular formation relationship: RO:0013001 UBERON:0002240 ! has synaptic IO in region spinal cord -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023108 @@ -34876,7 +34897,7 @@ is_a: CL:0011003 ! magnocellular neurosecretory cell intersection_of: CL:0011003 ! magnocellular neurosecretory cell intersection_of: capable_of GO:0036162 ! oxytocin production relationship: capable_of GO:0036162 ! oxytocin production -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023109 @@ -34887,7 +34908,7 @@ is_a: CL:0011003 ! magnocellular neurosecretory cell intersection_of: CL:0011003 ! magnocellular neurosecretory cell intersection_of: capable_of GO:0030103 ! vasopressin secretion relationship: capable_of GO:0030103 ! vasopressin secretion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023110 @@ -34898,7 +34919,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0001876 ! has soma location amygdala relationship: RO:0002100 UBERON:0001876 ! has soma location amygdala -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023111 @@ -34908,7 +34929,7 @@ is_a: CL:0000598 ! pyramidal neuron is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023112 @@ -34916,7 +34937,7 @@ name: vestibular afferent neuron def: "An afferent neuron of the vestibular system that innervate the base of the hair cell and increase or decrease their neural firing rate as the receptor cell is excited or inhibited." [PMID:2585041] is_a: CL:0000101 ! sensory neuron relationship: RO:0002120 CL:0000609 ! synapsed to vestibular hair cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023113 @@ -34925,7 +34946,7 @@ def: "A vestibular afferent neuron that makes bouton synapses to type II hair ce is_a: CL:4023112 ! vestibular afferent neuron relationship: has_part GO:0043195 ! terminal bouton relationship: RO:0002130 CL:0002069 ! has synaptic terminal in type II vestibular sensory cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023114 @@ -34934,7 +34955,7 @@ def: "A vestibular afferent neuron which posseses a unique postsynaptic terminal is_a: CL:4023112 ! vestibular afferent neuron relationship: has_part GO:0099096 ! vestibular calyx terminal relationship: RO:0002130 CL:0002070 ! has synaptic terminal in type I vestibular sensory cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023115 @@ -34948,7 +34969,7 @@ intersection_of: CL:0011113 ! spiral ganglion neuron intersection_of: RO:0002134 CL:0000589 ! innervates cochlear inner hair cell relationship: bearer_of PATO:0070006 ! cortical bipolar morphology relationship: RO:0002134 CL:0000589 ! innervates cochlear inner hair cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023116 @@ -34962,7 +34983,7 @@ intersection_of: CL:0011113 ! spiral ganglion neuron intersection_of: RO:0002134 CL:0000601 ! innervates cochlear outer hair cell relationship: bearer_of PATO:0070025 ! unipolar neuron morphology relationship: RO:0002134 CL:0000601 ! innervates cochlear outer hair cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023118 @@ -34976,8 +34997,8 @@ is_a: CL:4023017 ! sst GABAergic cortical interneuron relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5/6 non-Martinotti sst interneuron (Mus)" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023119 @@ -34988,7 +35009,7 @@ synonym: "dACs" EXACT [] synonym: "inverted amacrine cell" EXACT [] is_a: CL:0000561 ! amacrine cell relationship: RO:0002292 PR:000015426 ! expresses transcription factor SOX-2 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023120 @@ -35002,7 +35023,7 @@ is_a: CL:0002374 ! ear hair cell intersection_of: CL:0000202 ! auditory hair cell intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea relationship: part_of UBERON:0002227 ! spiral organ of cochlea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023121 @@ -35012,8 +35033,8 @@ subset: cellxgene_subset synonym: "long-range GABAergic interneuron" BROAD [] is_a: CL:4023017 ! sst GABAergic cortical interneuron relationship: RO:0002292 PR:000005444 ! expresses chondrolectin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "sst chodl cortical interneuron" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023122 @@ -35023,8 +35044,8 @@ comment: These cells were first identified in mouse. {xref="PMID:25303526"} synonym: "OxtrINs" RELATED OMO:0003000 [PMID:25303526] is_a: CL:4023017 ! sst GABAergic cortical interneuron relationship: RO:0002292 PR:000001635 ! expresses oxytocin receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: RO:0002175 NCBITaxon:10090 {xref="PMID:25303526"} +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023123 @@ -35035,8 +35056,8 @@ is_a: CL:4023130 ! kisspeptin neuron intersection_of: CL:4023130 ! kisspeptin neuron intersection_of: RO:0002100 UBERON:0001898 ! has soma location hypothalamus relationship: RO:0002100 UBERON:0001898 ! has soma location hypothalamus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023124 @@ -35046,8 +35067,8 @@ is_a: CL:4023062 ! dentate gyrus neuron is_a: CL:4023130 ! kisspeptin neuron intersection_of: CL:4023130 ! kisspeptin neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023125 @@ -35061,8 +35082,8 @@ intersection_of: RO:0002292 PR:000012526 ! expresses proenkephalin-B intersection_of: RO:0002292 PR:000016004 ! expresses tachykinin-3 relationship: RO:0002292 PR:000012526 ! expresses proenkephalin-B relationship: RO:0002292 PR:000016004 ! expresses tachykinin-3 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023127 @@ -35072,8 +35093,8 @@ is_a: CL:4023125 ! KNDy neuron intersection_of: CL:4023125 ! KNDy neuron intersection_of: RO:0002100 UBERON:0001932 ! has soma location arcuate nucleus of hypothalamus relationship: RO:0002100 UBERON:0001932 ! has soma location arcuate nucleus of hypothalamus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023128 @@ -35084,9 +35105,9 @@ is_a: CL:4023125 ! KNDy neuron intersection_of: CL:4023125 ! KNDy neuron intersection_of: RO:0002100 UBERON:8440005 ! has soma location rostral periventricular region of the third ventricle relationship: RO:0002100 UBERON:8440005 ! has soma location rostral periventricular region of the third ventricle -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 property_value: IAO:0000116 "In rats and mice, the anteroventral periventricular nucleus plus the periventricular nucleus make up the rostral periventricular region of the third ventricle (RP3V)." xsd:string {xref="WikipediaVersioned:Anteroventral_periventricular_nucleus&oldid=966137187"} +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023129 @@ -35096,8 +35117,8 @@ subset: eye_upper_slim synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023130 @@ -35109,8 +35130,8 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002292 PR:000009344 ! expresses metastasis-suppressor KiSS-1 relationship: RO:0002292 PR:000009344 ! expresses metastasis-suppressor KiSS-1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023154 @@ -35121,7 +35142,7 @@ is_a: CL:0000125 ! glial cell intersection_of: CL:0000125 ! glial cell intersection_of: has_part GO:0043209 ! myelin sheath relationship: has_part GO:0043209 ! myelin sheath -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023158 @@ -35131,8 +35152,8 @@ comment: Octopus cells respond only at the onset of a broad-band simple tonal st is_a: CL:2000029 ! central nervous system neuron relationship: RO:0002100 UBERON:0002831 ! has soma location posteroventral cochlear nucleus relationship: RO:0013001 UBERON:8440043 ! has synaptic IO in region superior paraolivary nucleus -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: IAO:0000116 "This term is restricted to the mammalian cochlear nucleus to disambiguate for cells of octopus." xsd:string +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023159 @@ -35142,7 +35163,7 @@ is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070061 ! double bouquet morphology relationship: bearer_of PATO:0070061 ! double bouquet morphology -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023160 @@ -35155,7 +35176,7 @@ is_a: CL:1001509 ! glycinergic neuron is_a: CL:2000029 ! central nervous system neuron relationship: RO:0002100 UBERON:0002829 ! has soma location dorsal cochlear nucleus relationship: RO:0002103 CL:0000120 ! synapsed by granule cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023161 @@ -35165,7 +35186,7 @@ is_a: CL:0000402 ! CNS interneuron is_a: CL:0000679 ! glutamatergic neuron relationship: bearer_of PATO:0070025 ! unipolar neuron morphology relationship: RO:0002100 UBERON:0002028 ! has soma location hindbrain -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023162 @@ -35174,7 +35195,7 @@ def: "A neuron found in the anterior part of the ventral cochlear nucleus that h is_a: CL:2000029 ! central nervous system neuron relationship: RO:0002100 UBERON:0002830 ! has soma location anteroventral cochlear nucleus relationship: RO:0013001 UBERON:0002128 ! has synaptic IO in region superior olivary complex -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023163 @@ -35182,7 +35203,7 @@ name: spherical bushy cell def: "A bushy cell that receives only few large excitatory endbulb synapses from auditory nerves. Spherical bush cells give excitatory input to the lateral and medial parts of the superior olive." [PMID:31881018, WikipediaVersioned:Bushy_cell&oldid=879061753] synonym: "SBC" RELATED OMO:0003000 [PMID:31881018] is_a: CL:4023162 ! bushy cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023164 @@ -35190,7 +35211,7 @@ name: globular bushy cell def: "A bushy cell that receives a large number of medium-sized synapses, called modified endbulbs. Globular bushy cells extend to the superior olive on both sides of the brainstem where they give input to the bipolar neurons." [PMID:31881018, WikipediaVersioned:Bushy_cell&oldid=879061753] synonym: "GBC" EXACT OMO:0003000 [PMID:31881018] is_a: CL:4023162 ! bushy cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023168 @@ -35200,14 +35221,14 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: part_of UBERON:0003942 ! somatosensory system relationship: part_of UBERON:0003942 ! somatosensory system -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023169 name: trigeminal neuron def: "A neuron that is responsible for sensation in the face or motor functions such as biting and chewing. Trigeminal neurons extend a single axon shaft along the lateral white matter of the hindbrain and spinal cord. The highly branched axons innervate the integument of the head." [PMID:22190641, WikipediaVersioned:Trigeminal_nerve&oldid=1099897926] is_a: CL:0000540 ! neuron -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023170 @@ -35218,7 +35239,7 @@ is_a: CL:4023168 ! somatosensory neuron is_a: CL:4023169 ! trigeminal neuron intersection_of: CL:4023169 ! trigeminal neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023171 @@ -35228,7 +35249,7 @@ is_a: CL:0000100 ! motor neuron is_a: CL:4023169 ! trigeminal neuron intersection_of: CL:0000100 ! motor neuron intersection_of: CL:4023169 ! trigeminal neuron -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023181 @@ -35239,7 +35260,7 @@ is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002319 ! neural cell relationship: part_of UBERON:0002139 ! subcommissural organ relationship: RO:0002292 PR:000015658 ! expresses SCO-spondin -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-2105-0715 +property_value: terms:contributor http://orcid.org/0000-0002-2105-0715 [Term] id: CL:4023187 @@ -35252,7 +35273,7 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0013615 ! has soma location koniocellular layer of dorsal nucleus of lateral geniculate body relationship: RO:0002100 UBERON:0013615 ! has soma location koniocellular layer of dorsal nucleus of lateral geniculate body -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023188 @@ -35262,9 +35283,9 @@ comment: There are midget bipolar cells of retina and midget ganglion cells of r subset: human_reference_atlas is_a: CL:0000740 ! retinal ganglion cell relationship: RO:0013001 UBERON:0013607 ! has synaptic IO in region parvocellular layer of dorsal nucleus of lateral geniculate body -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7655-4833" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7655-4833" xsd:string [Term] id: CL:4023189 @@ -35276,9 +35297,9 @@ synonym: "M cell" RELATED [] synonym: "M ganglion cell" RELATED [] is_a: CL:0000740 ! retinal ganglion cell relationship: RO:0013001 UBERON:0013606 ! has synaptic IO in region magnocellular layer of dorsal nucleus of lateral geniculate body -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7655-4833" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: terms:contributor "https://orcid.org/0000-0001-7655-4833" xsd:string [Term] id: CL:4028001 @@ -35290,7 +35311,7 @@ is_a: CL:2000016 ! lung microvascular endothelial cell intersection_of: CL:0002144 ! capillary endothelial cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0016405 ! pulmonary capillary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +property_value: terms:contributor https://orcid.org/0000-0002-3293-5463 creation_date: 2021-11-23T02:31:40Z [Term] @@ -35302,10 +35323,10 @@ synonym: "CAP1" RELATED OMO:0003000 [] synonym: "capillary 1 cell" BROAD [] synonym: "gCAP" RELATED OMO:0003000 [PMID:33057196] synonym: "general capillary cell" BROAD [PMID:33057196] -is_a: CL:0010003 ! epithelial cell of alveolus of lung is_a: CL:4028001 ! pulmonary capillary endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +relationship: part_of UBERON:0002299 ! alveolus of lung property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-3293-5463 creation_date: 2021-11-23T03:23:53Z [Term] @@ -35319,10 +35340,10 @@ synonym: "alveolar capillary cell" BROAD [] synonym: "capillary 2 cell" BROAD [] synonym: "Car4+ capillary endothelial cell" BROAD [] synonym: "CD34hi endothelial cells" BROAD [] -is_a: CL:0010003 ! epithelial cell of alveolus of lung is_a: CL:4028001 ! pulmonary capillary endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +relationship: part_of UBERON:0002299 ! alveolus of lung property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-3293-5463 creation_date: 2021-11-23T03:23:53Z [Term] @@ -35341,22 +35362,24 @@ synonym: "pulmonary lipofibroblast" BROAD [] is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:0002553 ! fibroblast of lung relationship: part_of UBERON:0002299 ! alveolus of lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9610-7627 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1425-877X -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8445-4565 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9610-7627 +property_value: terms:contributor https://orcid.org/0000-0002-1425-877X +property_value: terms:contributor https://orcid.org/0000-0002-3293-5463 +property_value: terms:contributor https://orcid.org/0000-0002-8445-4565 creation_date: 2021-12-09T15:34:13Z [Term] id: CL:4028006 -name: alveolar type 2 fibroblast cell +name: alveolar adventitial fibroblast def: "A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia." [PMID:26706109, PMID:28886382, PMID:29752282, PMID:30675802, PMID:33208946, PMID:33624948] subset: cellxgene_subset subset: human_reference_atlas synonym: "adventitial fibroblast" BROAD [] +synonym: "AdvF" RELATED OMO:0003000 [PMID:33208946] synonym: "AF2" RELATED OMO:0003000 [] synonym: "alveolar fibroblast" BROAD [] +synonym: "alveolar type 2 fibroblast cell" EXACT [] synonym: "MANC" RELATED OMO:0003000 [] synonym: "matrix fibroblast 2" BROAD [] synonym: "mesenchymal alveolar niche cell" BROAD [] @@ -35364,8 +35387,8 @@ synonym: "type-2 associated stromal cell" BROAD [] is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:0002553 ! fibroblast of lung relationship: part_of UBERON:0002299 ! alveolus of lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-3293-5463 creation_date: 2021-12-09T15:53:21Z [Term] @@ -35375,8 +35398,8 @@ namespace: cell def: "A cell that supports the development of a gamete by providing it cytoplasmic material (including entire organelles) by direct cross-membrane channels (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] xref: BTO:0000953 is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2022-06-08T15:29:54Z" xsd:dateTime +property_value: terms:contributor http://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2022-06-08T15:29:54Z" xsd:dateTime [Term] id: CL:4029002 @@ -35386,8 +35409,8 @@ def: "A gamete-nursing cell that derives from a germline cell (del Pino, 2021)." comment: Nurse cells were first described in insects, but recent works suggest they also exist in some mammals (Lei and Spradling, 2016). {xref="doi:10.1126/science.aad2156"} is_a: CL:0000039 ! germ line cell is_a: CL:4029001 ! gamete-nursing cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2022-06-08T15:32:29Z" xsd:dateTime +property_value: terms:contributor http://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2022-06-08T15:32:29Z" xsd:dateTime [Term] id: CL:4029003 @@ -35396,8 +35419,8 @@ namespace: cell def: "A gamete-nursing cell that derives from the somatic tissues of the gonad (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] comment: We follow what seems to be a common usage in the literature, which is to reserve the term “nurse cell” proper to cells from the germ line, hence the label “nurse-like”. This term encompasses pyriform cells described in reptiles, bird, and amphibians (del Pino, 2021); it does not encompass mammalian Sertoli cells, which do not appear to transfer cytoplasmic material to spermatogonia (França et al., 2016). {xref="doi:10.1111/andr.12165"} is_a: CL:4029001 ! gamete-nursing cell -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2022-06-08T15:38:03Z" xsd:dateTime +property_value: terms:contributor http://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2022-06-08T15:38:03Z" xsd:dateTime [Term] id: CL:4030000 @@ -35420,7 +35443,7 @@ is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002370 ! thymus relationship: part_of UBERON:0002370 ! thymus -property_value: http://purl.org/dc/terms/date "2022-07-08T11:39:38Z" xsd:dateTime +property_value: terms:date "2022-07-08T11:39:38Z" xsd:dateTime [Term] id: CL:4030002 @@ -35440,14 +35463,14 @@ name: interstitial cell of thymus def: "A cell that makes up the loose connective tissue of the thymus." [doi:10.1038/s41467-020-20082-7] synonym: "thymic interstitial cell" EXACT [] is_a: CL:4030001 ! stromal cell of thymus -property_value: http://purl.org/dc/terms/date "2022-07-08T11:48:36Z" xsd:dateTime +property_value: terms:date "2022-07-08T11:48:36Z" xsd:dateTime [Term] id: CL:4030004 name: thymic nurse cell -def: "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." [https://en.wikipedia.org/wiki/Thymic_nurse_cell] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} +def: "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." [https://en.wikipedia.org/wiki/Thymic_nurse_cell] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} is_a: CL:0002293 ! epithelial cell of thymus -property_value: http://purl.org/dc/terms/date "2022-02-18T12:43:20Z" xsd:dateTime +property_value: terms:date "2022-02-18T12:43:20Z" xsd:dateTime [Term] id: CL:4030005 @@ -35459,87 +35482,100 @@ is_a: CL:0002201 ! renal beta-intercalated cell is_a: CL:1000715 ! kidney cortex collecting duct intercalated cell intersection_of: CL:0002201 ! renal beta-intercalated cell intersection_of: part_of UBERON:0004203 ! cortical collecting duct -property_value: http://purl.org/dc/terms/date "2022-09-14T16:19:11Z" xsd:dateTime +property_value: terms:date "2022-09-14T16:19:11Z" xsd:dateTime [Term] id: CL:4030006 name: fallopian tube secretory epithelial cell -def: "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell." [https://doi.org/10.1186/1477-7827-7-129, https://doi.org/10.3390/cells8080933, https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} +def: "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell." [https://doi.org/10.1186/1477-7827-7-129, https://doi.org/10.3390/cells8080933, https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} comment: The other cell types of the fallopian tube epithelium include the ciliated cell and the intercalary cell, or peg cell. The fallopian tube secretory epithelial cell type has been implicated as a source of high-grade serous ovarian carcinoma. {xref="https://doi.org/10.1016/j.ccr.2013.10.013", xref="https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"} subset: human_reference_atlas synonym: "oviduct secretory epithelial cell" BROAD [] synonym: "uterine tube secretory epithelial cell" EXACT [] is_a: CL:1001591 ! oviduct glandular cell -property_value: http://purl.org/dc/terms/date "2022-03-03T10:39:31Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-03-03T10:39:31Z" xsd:dateTime [Term] id: CL:4030007 name: fallopian tube ciliated cell -def: "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell." [PMID:16565155] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} +def: "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell." [PMID:16565155] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} subset: human_reference_atlas synonym: "oviduct ciliated cell" BROAD [] synonym: "uterine tube ciliated epithelial cell" EXACT [] is_a: CL:0005012 ! multi-ciliated epithelial cell relationship: part_of UBERON:0007589 ! ciliated columnar oviduct epithelium -property_value: http://purl.org/dc/terms/date "2022-03-08T12:40:19Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-03-08T12:40:19Z" xsd:dateTime [Term] id: CL:4030008 name: pronephric podocyte -def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the pronephros." [PMID:10322630] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-2244-7917"} +def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the pronephros." [PMID:10322630] {terms:contributor="https://orcid.org/0000-0002-2244-7917"} synonym: "pronephric glomerular visceral epithelial cell" EXACT [ZFA:0001673] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0002120 ! pronephros relationship: part_of UBERON:0002120 ! pronephros -property_value: http://purl.org/dc/terms/date "2022-03-11T14:38:32Z" xsd:dateTime +property_value: terms:date "2022-03-11T14:38:32Z" xsd:dateTime [Term] id: CL:4030009 name: epithelial cell of proximal tubule segment 1 -def: "Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium." [PMID:31249312] +def: "A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex." [PMID:23799132, PMID:23897681, PMID:31249312] subset: cellxgene_subset subset: human_reference_atlas synonym: "epithelial cell of segment 1 of proximal tubule" EXACT [] -is_a: CL:0002306 ! epithelial cell of proximal tubule -property_value: http://purl.org/dc/terms/date "2022-05-10T13:14:00Z" xsd:dateTime +is_a: CL:1000838 ! kidney proximal convoluted tubule epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: has_part GO:0005903 ! brush border +intersection_of: part_of UBERON:0004196 ! proximal convoluted tubule segment 1 +relationship: part_of UBERON:0004196 ! proximal convoluted tubule segment 1 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-10T13:14:00Z" xsd:dateTime [Term] id: CL:4030010 name: epithelial cell of proximal tubule segment 2 -def: "Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium." [PMID:31249312] +def: "A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate." [PMID:23799132, PMID:23897681, PMID:31249312, PMID:31253652] subset: human_reference_atlas synonym: "epithelial cell of segment 2 of proximal tubule" EXACT [] -is_a: CL:0002306 ! epithelial cell of proximal tubule -property_value: http://purl.org/dc/terms/date "2022-05-10T13:26:13Z" xsd:dateTime +is_a: CL:1000838 ! kidney proximal convoluted tubule epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: has_part GO:0005903 ! brush border +intersection_of: part_of UBERON:0004197 ! proximal convoluted tubule segment 2 +relationship: part_of UBERON:0004197 ! proximal convoluted tubule segment 2 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-10T13:26:13Z" xsd:dateTime [Term] id: CL:4030011 name: epithelial cell of proximal tubule segment 3 -def: "Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium." [PMID:31249312] +def: "A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium, which extends from the medullary rays of the renal cortex into the outer medulla." [PMID:23799132, PMID:31249312] +comment: The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury. {xref="PMID:31249312"} subset: cellxgene_subset subset: human_reference_atlas synonym: "epithelial cell of segment 3 of proximal tubule" EXACT [] -is_a: CL:0002306 ! epithelial cell of proximal tubule -property_value: http://purl.org/dc/terms/date "2022-05-10T13:31:06Z" xsd:dateTime +is_a: CL:0002307 ! brush border cell of the proximal tubule +is_a: CL:1000839 ! kidney proximal straight tubule epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: has_part GO:0005903 ! brush border +intersection_of: part_of UBERON:0001290 ! proximal straight tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-10T13:31:06Z" xsd:dateTime [Term] id: CL:4030012 name: kidney loop of Henle short descending thin limb epithelial cell -def: "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2." [PMID:33769951] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-2804-127X"} +def: "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2." [PMID:33769951] {terms:contributor="https://orcid.org/0000-0003-2804-127X"} subset: human_reference_atlas synonym: "epithelial cell of the descending thin limb of the short loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005099 ! short descending thin limb relationship: part_of UBERON:0005099 ! short descending thin limb -property_value: http://purl.org/dc/terms/date "2022-05-13T11:00:29Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-13T11:00:29Z" xsd:dateTime [Term] id: CL:4030013 @@ -35549,8 +35585,8 @@ subset: human_reference_atlas synonym: "epithelial cell of the outer medulla of the long descending limb of the loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell relationship: part_of UBERON:0005100 ! long descending thin limb -property_value: http://purl.org/dc/terms/date "2022-05-13T11:11:07Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-13T11:11:07Z" xsd:dateTime [Term] id: CL:4030014 @@ -35560,21 +35596,21 @@ subset: human_reference_atlas synonym: "epithelial cell of the inner medulla of the long descending limb of the loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell relationship: part_of UBERON:0005100 ! long descending thin limb -property_value: http://purl.org/dc/terms/date "2022-05-13T11:16:54Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-13T11:16:54Z" xsd:dateTime [Term] id: CL:4030015 name: kidney collecting duct alpha-intercalated cell -def: "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule." [PMID:31249312, PMID:9890303] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-2804-127X"} +def: "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule." [PMID:31249312, PMID:9890303] {terms:contributor="https://orcid.org/0000-0003-2804-127X"} subset: human_reference_atlas synonym: "kidney collecting duct intercalated cell type A" EXACT [PMID:9890303] is_a: CL:0005011 ! renal alpha-intercalated cell is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005011 ! renal alpha-intercalated cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -property_value: http://purl.org/dc/terms/date "2022-05-31T11:15:10Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-05-31T11:15:10Z" xsd:dateTime [Term] id: CL:4030016 @@ -35586,8 +35622,8 @@ is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005101 ! early distal convoluted tubule relationship: part_of UBERON:0005101 ! early distal convoluted tubule -property_value: http://purl.org/dc/terms/date "2022-06-21T12:47:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-21T12:47:48Z" xsd:dateTime [Term] id: CL:4030017 @@ -35600,8 +35636,8 @@ is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005102 ! late distal convoluted tubule relationship: part_of UBERON:0005102 ! late distal convoluted tubule -property_value: http://purl.org/dc/terms/date "2022-06-21T13:51:46Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-21T13:51:46Z" xsd:dateTime [Term] id: CL:4030018 @@ -35613,8 +35649,8 @@ is_a: CL:0005009 ! renal principal cell is_a: CL:1000768 ! kidney connecting tubule epithelial cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -property_value: http://purl.org/dc/terms/date "2022-06-27T15:25:10Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-27T15:25:10Z" xsd:dateTime [Term] id: CL:4030019 @@ -35625,8 +35661,8 @@ is_a: CL:0005010 ! renal intercalated cell is_a: CL:1000768 ! kidney connecting tubule epithelial cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -property_value: http://purl.org/dc/terms/date "2022-06-29T11:25:22Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-29T11:25:22Z" xsd:dateTime [Term] id: CL:4030020 @@ -35639,8 +35675,8 @@ is_a: CL:0005011 ! renal alpha-intercalated cell is_a: CL:4030019 ! kidney connecting tubule intercalated cell intersection_of: CL:0005011 ! renal alpha-intercalated cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -property_value: http://purl.org/dc/terms/date "2022-06-29T12:48:43Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-29T12:48:43Z" xsd:dateTime [Term] id: CL:4030021 @@ -35653,8 +35689,8 @@ is_a: CL:0002201 ! renal beta-intercalated cell is_a: CL:4030019 ! kidney connecting tubule intercalated cell intersection_of: CL:0002201 ! renal beta-intercalated cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -property_value: http://purl.org/dc/terms/date "2022-06-29T14:31:18Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-29T14:31:18Z" xsd:dateTime [Term] id: CL:4030022 @@ -35667,8 +35703,8 @@ is_a: CL:1000682 ! kidney medulla interstitial cell is_a: CL:1000692 ! kidney interstitial fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005211 ! renal medulla interstitium -property_value: http://purl.org/dc/terms/date "2022-07-05T12:13:40Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-07-05T12:13:40Z" xsd:dateTime [Term] id: CL:4030023 @@ -35679,15 +35715,15 @@ synonym: "hillock cell of respiratory tract" NARROW [] is_a: CL:0002368 ! respiratory epithelial cell is_a: CL:4030024 ! hillock cell intersection_of: CL:4030024 ! hillock cell -intersection_of: part_of UBERON:0000065 ! respiratory tract -property_value: http://purl.org/dc/terms/date "2022-06-06T08:31:09Z" xsd:dateTime +intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium +property_value: terms:date "2022-06-06T08:31:09Z" xsd:dateTime [Term] id: CL:4030024 name: hillock cell def: "An epithelial, transitional cell type between basal and secretory; located in stratified, non-ciliated structures (called hillocks) with high cell turnover in epithelium. In some mammalian species, this cell type has been noted to express KRT13 and is postulated to play a role in squamous barrier function and immunomodulation." [PMID:30069044] is_a: CL:0000066 ! epithelial cell -property_value: http://purl.org/dc/terms/date "2022-06-24T14:52:24Z" xsd:dateTime +property_value: terms:date "2022-06-24T14:52:24Z" xsd:dateTime [Term] id: CL:4030025 @@ -35699,7 +35735,7 @@ is_a: CL:1000681 ! kidney cortex interstitial cell is_a: CL:1000692 ! kidney interstitial fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005270 ! renal cortex interstitium -property_value: http://purl.org/dc/terms/date "2022-07-05T15:50:17Z" xsd:dateTime +property_value: terms:date "2022-07-05T15:50:17Z" xsd:dateTime [Term] id: CL:4030026 @@ -35711,7 +35747,7 @@ is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000677 ! gut absorptive cell relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens relationship: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) -property_value: http://purl.org/dc/terms/date "2022-09-07T12:34:20Z" xsd:dateTime +property_value: terms:date "2022-09-07T12:34:20Z" xsd:dateTime [Term] id: CL:4030027 @@ -35723,7 +35759,7 @@ is_a: CL:0000561 ! amacrine cell is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0000561 ! amacrine cell intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -property_value: http://purl.org/dc/terms/date "2022-10-17T12:35:11Z" xsd:dateTime +property_value: terms:date "2022-10-17T12:35:11Z" xsd:dateTime [Term] id: CL:4030028 @@ -35736,8 +35772,8 @@ is_a: CL:0000561 ! amacrine cell is_a: CL:1001509 ! glycinergic neuron intersection_of: CL:0000561 ! amacrine cell intersection_of: capable_of GO:0061537 ! glycine secretion, neurotransmission -property_value: http://purl.org/dc/terms/date "2022-10-17T12:40:06Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-10-17T12:40:06Z" xsd:dateTime [Term] id: CL:4030029 @@ -35748,7 +35784,7 @@ is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/date "2022-11-04T14:40:00Z" xsd:dateTime +property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime [Term] id: CL:4030030 @@ -35757,8 +35793,8 @@ def: "A blood lymphocyte located in the flowing, circulating blood of the body." is_a: CL:4030029 ! blood lymphocyte relationship: RO:0001025 UBERON:0013755 ! located in arterial blood relationship: RO:0001025 UBERON:0013756 ! located in venous blood -property_value: http://purl.org/dc/terms/date "2022-11-14T10:08:14Z" xsd:dateTime property_value: seeAlso "https://github.com/obophenotype/cell-ontology/pull/1725" xsd:string +property_value: terms:date "2022-11-14T10:08:14Z" xsd:dateTime [Term] id: CL:4030031 @@ -35768,7 +35804,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue -property_value: http://purl.org/dc/terms/date "2022-11-30T14:35:08Z" xsd:dateTime +property_value: terms:date "2022-11-30T14:35:08Z" xsd:dateTime [Term] id: CL:4030032 @@ -35785,8 +35821,8 @@ is_a: CL:4030031 ! interstitial cell intersection_of: CL:4030031 ! interstitial cell intersection_of: part_of UBERON:0000946 ! cardiac valve relationship: capable_of GO:0070278 ! extracellular matrix constituent secretion -property_value: http://purl.org/dc/terms/date "2022-12-06T14:18:45Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-12-06T14:18:45Z" xsd:dateTime [Term] id: CL:4030033 @@ -35799,7 +35835,7 @@ is_a: CL:0010008 ! cardiac endothelial cell is_a: CL:1000147 ! cardiac valve cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000946 ! cardiac valve -property_value: http://purl.org/dc/terms/date "2022-12-09T11:58:49Z" xsd:dateTime +property_value: terms:date "2022-12-09T11:58:49Z" xsd:dateTime [Term] id: CL:4030034 @@ -35810,7 +35846,7 @@ is_a: CL:0000064 ! ciliated cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium relationship: part_of UBERON:0004802 ! respiratory tract epithelium -property_value: http://purl.org/dc/terms/date "2023-01-25T11:06:01Z" xsd:dateTime +property_value: terms:date "2023-01-25T11:06:01Z" xsd:dateTime [Term] id: CL:4030035 @@ -35821,7 +35857,7 @@ is_a: CL:0000034 ! stem cell is_a: CL:0002148 ! dental pulp cell intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0001754 ! dental pulp -property_value: http://purl.org/dc/terms/date "2023-01-10T14:02:02Z" xsd:dateTime +property_value: terms:date "2023-01-10T14:02:02Z" xsd:dateTime [Term] id: CL:4030036 @@ -35831,7 +35867,7 @@ synonym: "round spermatid" EXACT [https://doi.org/10.1016/B978-0-323-01970-5.500 is_a: CL:0000018 ! spermatid relationship: capable_of GO:0007286 ! spermatid development relationship: part_of UBERON:0000079 ! male reproductive system -property_value: http://purl.org/dc/terms/date "2023-02-01T13:56:00Z" xsd:dateTime +property_value: terms:date "2023-02-01T13:56:00Z" xsd:dateTime [Term] id: CL:4030037 @@ -35842,7 +35878,7 @@ is_a: CL:0000018 ! spermatid relationship: capable_of GO:0007286 ! spermatid development relationship: part_of UBERON:0000079 ! male reproductive system relationship: RO:0002202 CL:4030036 ! develops from early spermatid -property_value: http://purl.org/dc/terms/date "2023-02-01T14:02:15Z" xsd:dateTime +property_value: terms:date "2023-02-01T14:02:15Z" xsd:dateTime [Term] id: CL:4030038 @@ -35857,7 +35893,7 @@ relationship: part_of UBERON:0008404 ! proximal tubular epithelium relationship: RO:0002292 PR:000001786 ! expresses prominin-1 relationship: RO:0002292 PR:000001932 ! expresses signal transducer CD24 relationship: RO:0002292 PR:000017298 ! expresses vimentin -property_value: http://purl.org/dc/terms/date "2023-03-07T14:17:39Z" xsd:dateTime +property_value: terms:date "2023-03-07T14:17:39Z" xsd:dateTime [Term] id: CL:4030039 @@ -35867,7 +35903,7 @@ comment: In humans, a von Economo neuron is restricted to layer 5 of the anterio synonym: "VEN" RELATED OMO:0003000 [PMID:32127543] is_a: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070006 ! cortical bipolar morphology -property_value: http://purl.org/dc/terms/date "2023-05-25T07:29:21Z" xsd:dateTime +property_value: terms:date "2023-05-25T07:29:21Z" xsd:dateTime [Term] id: CL:4030040 @@ -35883,7 +35919,7 @@ intersection_of: CL:0000064 ! ciliated cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004811 ! endometrium epithelium relationship: part_of UBERON:0004811 ! endometrium epithelium -property_value: http://purl.org/dc/terms/date "2023-02-09T11:25:14Z" xsd:dateTime +property_value: terms:date "2023-02-09T11:25:14Z" xsd:dateTime [Term] id: CL:4030041 @@ -35891,7 +35927,7 @@ name: luminal endometrial ciliated epithelial cell def: "A ciliated cell of the endometrial luminal epithelium." [doi:10.1038/s41591-020-1040-z] is_a: CL:4030040 ! endometrial ciliated epithelial cell relationship: part_of UBERON:0011949 ! endometrium luminal epithelium -property_value: http://purl.org/dc/terms/date "2023-02-09T11:34:42Z" xsd:dateTime +property_value: terms:date "2023-02-09T11:34:42Z" xsd:dateTime [Term] id: CL:4030042 @@ -35899,7 +35935,7 @@ name: glandular endometrial ciliated epithelial cell def: "A ciliated cell of the endometrial glandular epithelium." [doi:10.1038/s41591-020-1040-z] is_a: CL:4030040 ! endometrial ciliated epithelial cell relationship: part_of UBERON:0012276 ! endometrium glandular epithelium -property_value: http://purl.org/dc/terms/date "2023-02-09T11:37:30Z" xsd:dateTime +property_value: terms:date "2023-02-09T11:37:30Z" xsd:dateTime [Term] id: CL:4030043 @@ -35910,7 +35946,7 @@ synonym: "D1-matrix" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D1M" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "matrix D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023026 ! direct pathway medium spiny neuron -property_value: http://purl.org/dc/terms/date "2023-06-02T14:05:03Z" xsd:dateTime +property_value: terms:date "2023-06-02T14:05:03Z" xsd:dateTime [Term] id: CL:4030047 @@ -35921,7 +35957,7 @@ synonym: "D2-matrix" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D2M" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "matrix D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023029 ! indirect pathway medium spiny neuron -property_value: http://purl.org/dc/terms/date "2023-06-02T14:40:25Z" xsd:dateTime +property_value: terms:date "2023-06-02T14:40:25Z" xsd:dateTime [Term] id: CL:4030048 @@ -35933,7 +35969,7 @@ synonym: "D1S" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D1 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023026 ! direct pathway medium spiny neuron -property_value: http://purl.org/dc/terms/date "2023-06-02T14:50:43Z" xsd:dateTime +property_value: terms:date "2023-06-02T14:50:43Z" xsd:dateTime [Term] id: CL:4030049 @@ -35945,7 +35981,7 @@ synonym: "D2S" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D2 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023029 ! indirect pathway medium spiny neuron -property_value: http://purl.org/dc/terms/date "2023-06-02T15:03:08Z" xsd:dateTime +property_value: terms:date "2023-06-02T15:03:08Z" xsd:dateTime [Term] id: CL:4030050 @@ -35961,7 +35997,7 @@ is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005382 ! has soma location dorsal striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor -property_value: http://purl.org/dc/terms/date "2023-06-02T15:19:45Z" xsd:dateTime +property_value: terms:date "2023-06-02T15:19:45Z" xsd:dateTime [Term] id: CL:4030051 @@ -35975,7 +36011,7 @@ is_a: BFO:0000002 is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor -property_value: http://purl.org/dc/terms/date "2023-06-14T13:03:50Z" xsd:dateTime +property_value: terms:date "2023-06-14T13:03:50Z" xsd:dateTime [Term] id: CL:4030052 @@ -35990,7 +36026,7 @@ is_a: BFO:0000002 is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor -property_value: http://purl.org/dc/terms/date "2023-06-14T13:27:51Z" xsd:dateTime +property_value: terms:date "2023-06-14T13:27:51Z" xsd:dateTime [Term] id: CL:4030053 @@ -36001,7 +36037,7 @@ synonym: "D1-ICj" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:0000120 ! granule cell is_a: CL:0002613 ! striatum neuron relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor -property_value: http://purl.org/dc/terms/date "2023-06-14T13:37:45Z" xsd:dateTime +property_value: terms:date "2023-06-14T13:37:45Z" xsd:dateTime [Term] id: CL:4030054 @@ -36015,7 +36051,7 @@ is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor relationship: RO:0002292 PR:000001666 ! expresses relaxin receptor 1 -property_value: http://purl.org/dc/terms/date "2023-06-14T14:46:08Z" xsd:dateTime +property_value: terms:date "2023-06-14T14:46:08Z" xsd:dateTime [Term] id: CL:4030055 @@ -36026,9 +36062,9 @@ subset: human_reference_atlas synonym: "urothelial intermediate cell" EXACT [doi:10.1007/978-3-030-14366-4_8] xref: FMA:84155 is_a: CL:0000731 ! urothelial cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0003-3065-9183" xsd:string -property_value: http://purl.org/dc/terms/date "2023-06-16T07:53:43Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0003-3065-9183" xsd:string +property_value: terms:date "2023-06-16T07:53:43Z" xsd:dateTime [Term] id: CL:4030056 @@ -36040,9 +36076,9 @@ synonym: "facet cell of urothelium" EXACT [doi:10.1038/s41385-022-00565-0] synonym: "superficial cell of urothelium" EXACT [doi:10.1038/s41385-022-00565-0] xref: FMA:84149 is_a: CL:0000731 ! urothelial cell -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0003-3065-9183" xsd:string -property_value: http://purl.org/dc/terms/date "2023-06-16T07:59:43Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor "https://orcid.org/0000-0003-3065-9183" xsd:string +property_value: terms:date "2023-06-16T07:59:43Z" xsd:dateTime [Term] id: CL:4030057 @@ -36054,7 +36090,7 @@ synonym: "eccentric spiny projection neuron" EXACT [doi:10.1016/j.cell.2018.07.0 synonym: "eccentric SPN" RELATED OMO:0003000 [doi:10.1016/j.cell.2018.07.028] synonym: "eSPN" RELATED OMO:0003000 [doi:10.1016/j.cell.2018.07.028] is_a: CL:1001474 ! medium spiny neuron -property_value: http://purl.org/dc/terms/date "2023-06-23T14:59:36Z" xsd:dateTime +property_value: terms:date "2023-06-23T14:59:36Z" xsd:dateTime [Term] id: CL:4030058 @@ -36067,8 +36103,8 @@ is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex relationship: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3308-6245 -property_value: http://purl.org/dc/terms/date "2023-09-26T12:27:14Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-3308-6245 +property_value: terms:date "2023-09-26T12:27:14Z" xsd:dateTime [Term] id: CL:4030059 @@ -36081,9 +36117,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III relationship: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:10:21Z" xsd:dateTime property_value: IAO:0000028 "L2/3 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:10:21Z" xsd:dateTime [Term] id: CL:4030060 @@ -36094,9 +36130,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005391 ! has soma location cortical layer II relationship: RO:0002100 UBERON:0005391 ! has soma location cortical layer II -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:10:36Z" xsd:dateTime property_value: IAO:0000028 "L2 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:10:36Z" xsd:dateTime [Term] id: CL:4030061 @@ -36107,9 +36143,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005392 ! has soma location cortical layer III relationship: RO:0002100 UBERON:0005392 ! has soma location cortical layer III -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:10:47Z" xsd:dateTime property_value: IAO:0000028 "L3 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:10:47Z" xsd:dateTime [Term] id: CL:4030062 @@ -36120,9 +36156,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:8440001 ! has soma location cortical layer IV/V relationship: RO:0002100 UBERON:8440001 ! has soma location cortical layer IV/V -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:11:04Z" xsd:dateTime property_value: IAO:0000028 "L4/5 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:11:04Z" xsd:dateTime [Term] id: CL:4030063 @@ -36134,9 +36170,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV relationship: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:11:25Z" xsd:dateTime property_value: IAO:0000028 "L4 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:11:25Z" xsd:dateTime [Term] id: CL:4030064 @@ -36148,9 +36184,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:11:59Z" xsd:dateTime property_value: IAO:0000028 "L5 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:11:59Z" xsd:dateTime [Term] id: CL:4030065 @@ -36162,9 +36198,9 @@ is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-10-10T14:12:23Z" xsd:dateTime property_value: IAO:0000028 "L6 IT" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-10-10T14:12:23Z" xsd:dateTime [Term] id: CL:4030066 @@ -36178,8 +36214,8 @@ intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000084 ! ureteric bud relationship: part_of UBERON:0000084 ! ureteric bud relationship: participates_in GO:2001013 {xref="PMID:9374839"} ! epithelial cell proliferation involved in renal tubule morphogenesis -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-1425-877X" xsd:string -property_value: http://purl.org/dc/terms/date "2023-10-13T11:22:42Z" xsd:dateTime +property_value: terms:contributor "https://orcid.org/0000-0002-1425-877X" xsd:string +property_value: terms:date "2023-10-13T11:22:42Z" xsd:dateTime [Term] id: CL:4030067 @@ -36190,8 +36226,8 @@ is_a: CL:4023012 ! near-projecting glutamatergic cortical neuron intersection_of: CL:4023012 ! near-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-11-17T11:35:06Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-11-17T11:35:06Z" xsd:dateTime [Term] id: CL:4030068 @@ -36208,9 +36244,9 @@ intersection_of: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neu intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI intersection_of: RO:0002292 PR:000004919 ! expresses relationship: RO:0002292 PR:000004919 ! expresses -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 -property_value: http://purl.org/dc/terms/date "2023-11-23T09:16:14Z" xsd:dateTime property_value: IAO:0000028 "L6 IT Car3" xsd:string +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:date "2023-11-23T09:16:14Z" xsd:dateTime [Term] id: CL:4032000 @@ -36224,9 +36260,9 @@ synonym: "prostate club cell" EXACT [PMID:30566875] is_a: BFO:0000002 is_a: CL:1000296 ! epithelial cell of urethra relationship: RO:0002292 PR:000014505 ! expresses uteroglobin -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-6757-4744 property_value: IAO:0000116 "The term \"club-like\" is used to disambiguate from club cells which CL defines as a type of bronchial epithelial cell. This seems to reflect common usage of club cell when used without location (club cell seems to mean bronchial club cell, unless it is proceded or preceded by something that says it is not bronchial). In the literature, the name \"club-like\" isn't used." xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor http://orcid.org/0000-0001-6757-4744 [Term] id: CL:4032001 @@ -36240,19 +36276,19 @@ intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neur intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000013879 ! expresses reelin relationship: RO:0002292 PR:000013879 ! expresses reelin -property_value: http://purl.org/dc/terms/contributor "http://orcid.org/0000-0001-5501-853X" xsd:string -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-6757-4744 -property_value: http://purl.org/dc/terms/contributor "http://orcid.org/0000-0001-7476-6306" xsd:string +property_value: terms:contributor "http://orcid.org/0000-0001-5501-853X" xsd:string +property_value: terms:contributor http://orcid.org/0000-0001-6757-4744 +property_value: terms:contributor "http://orcid.org/0000-0001-7476-6306" xsd:string [Term] id: CL:4033000 name: endothelial cell of venule of lymph node def: "A(n) endothelial cell that is part of a(n) venule of lymph node." [PMID:28217126] -is_a: CL:0000115 ! endothelial cell +is_a: CL:1000414 ! endothelial cell of venule intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410041 ! venule of lymph node relationship: part_of UBERON:8410041 ! venule of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033001 @@ -36262,7 +36298,7 @@ is_a: CL:1000412 ! endothelial cell of arteriole intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410042 ! arteriole of lymph node relationship: part_of UBERON:8410042 ! arteriole of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033002 @@ -36273,7 +36309,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0011184 ! epithelium of crypt of Lieberkuhn relationship: part_of UBERON:0011184 ! epithelium of crypt of Lieberkuhn -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033003 @@ -36285,8 +36321,8 @@ is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:8410043 ! bronchus submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033004 @@ -36296,7 +36332,7 @@ is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012419 ! taenia coli relationship: part_of UBERON:0012419 ! taenia coli -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033005 @@ -36308,18 +36344,18 @@ is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:8410043 ! bronchus submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033006 name: endothelial cell of efferent lymphatic vessel def: "A(n) endothelial cell that is part of a(n) efferent lymphatic vessel." [PMID:32094869] -is_a: CL:0000115 ! endothelial cell +is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0010397 ! efferent lymphatic vessel relationship: part_of UBERON:0010397 ! efferent lymphatic vessel -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033007 @@ -36331,8 +36367,8 @@ is_a: CL:0002208 ! brush cell of bronchus intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033008 @@ -36343,8 +36379,8 @@ is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0002543 ! vein endothelial cell intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033009 @@ -36356,21 +36392,22 @@ is_a: CL:1000312 ! bronchial goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033010 name: neuroendocrine cell of epithelium of lobar bronchus def: "A(n) neuroendocrine cell that is part of a(n) epithelium of lobar bronchus." [PMID:26711336, PMID:33355253] subset: human_reference_atlas +is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:1000223 ! lung neuroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033011 @@ -36380,7 +36417,7 @@ is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012398 ! large intestine smooth muscle circular layer relationship: part_of UBERON:0012398 ! large intestine smooth muscle circular layer -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033012 @@ -36390,7 +36427,7 @@ is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012399 ! large intestine smooth muscle longitudinal layer relationship: part_of UBERON:0012399 ! large intestine smooth muscle longitudinal layer -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033013 @@ -36400,7 +36437,7 @@ is_a: CL:0000312 ! keratinocyte intersection_of: CL:0000312 ! keratinocyte intersection_of: part_of UBERON:0010402 ! epidermis suprabasal layer relationship: part_of UBERON:0010402 ! epidermis suprabasal layer -property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor http://orcid.org/0000-0001-6677-8489 creation_date: 2023-02-02T11:17:04Z [Term] @@ -36415,9 +36452,9 @@ synonym: "FTESC" EXACT OMO:0003000 [PMID:22911892] synonym: "intercalary cell" EXACT [PMID:22911892] is_a: CL:0000066 ! epithelial cell relationship: part_of UBERON:0004804 ! oviduct epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-02T15:07:12Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-02T15:07:12Z" xsd:dateTime [Term] id: CL:4033015 @@ -36431,8 +36468,8 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-03-02T14:38:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-03-02T14:38:32Z" xsd:dateTime [Term] id: CL:4033016 @@ -36447,10 +36484,10 @@ is_a: BFO:0000002 is_a: CL:0000186 ! myofibroblast cell relationship: part_of UBERON:0000114 ! lung connective tissue relationship: participates_in GO:0048286 ! lung alveolus development -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T09:17:47Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T09:17:47Z" xsd:dateTime [Term] id: CL:4033017 @@ -36461,10 +36498,10 @@ is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002186 ! bronchiole relationship: part_of UBERON:0004515 ! smooth muscle tissue of bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T09:38:17Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T09:38:17Z" xsd:dateTime [Term] id: CL:4033018 @@ -36480,10 +36517,10 @@ is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0000556 ! megakaryocyte intersection_of: part_of UBERON:0000114 ! lung connective tissue relationship: part_of UBERON:0000114 ! lung connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T11:31:23Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T11:31:23Z" xsd:dateTime [Term] id: CL:4033019 @@ -36493,9 +36530,9 @@ comment: The axons of a blue cone bipolar cell terminate close to the ganglion c subset: human_reference_atlas synonym: "BB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T09:48:15Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T09:48:15Z" xsd:dateTime [Term] id: CL:4033020 @@ -36508,10 +36545,10 @@ is_a: CL:4033037 ! mucus secreting cell of tracheobronchial tree submucosal glan intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:0005203 ! trachea gland relationship: part_of UBERON:0005203 ! trachea gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T13:03:13Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T13:03:13Z" xsd:dateTime [Term] id: CL:4033021 @@ -36523,10 +36560,10 @@ is_a: CL:0000307 ! tracheal epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0005203 ! trachea gland relationship: part_of UBERON:0005203 ! trachea gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T13:36:43Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T13:36:43Z" xsd:dateTime [Term] id: CL:4033022 @@ -36539,10 +36576,10 @@ is_a: CL:4033037 ! mucus secreting cell of tracheobronchial tree submucosal glan intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:8410043 ! bronchus submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T15:12:52Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T15:12:52Z" xsd:dateTime [Term] id: CL:4033023 @@ -36551,10 +36588,10 @@ def: "An epithelial cell that is part of a collecting duct of an airway submucos subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell relationship: part_of UBERON:8410077 ! airway submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T15:20:28Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T15:20:28Z" xsd:dateTime [Term] id: CL:4033024 @@ -36563,10 +36600,10 @@ def: "A basal cell that is part of a duct of an airway submucosal gland." [PMID: subset: human_reference_atlas is_a: CL:0000646 ! basal cell relationship: part_of UBERON:8410077 ! airway submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-9185-3994" xsd:string -property_value: http://purl.org/dc/terms/date "2023-03-16T15:51:39Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor "https://orcid.org/0000-0002-9185-3994" xsd:string +property_value: terms:date "2023-03-16T15:51:39Z" xsd:dateTime [Term] id: CL:4033025 @@ -36577,10 +36614,10 @@ is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0008305 ! outer fibrous layer of perichondrium relationship: part_of UBERON:0008305 ! outer fibrous layer of perichondrium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T16:12:50Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T16:12:50Z" xsd:dateTime [Term] id: CL:4033026 @@ -36592,10 +36629,10 @@ is_a: CL:0002553 ! fibroblast of lung is_a: CL:4033025 ! perichondrial fibroblast intersection_of: CL:4033025 ! perichondrial fibroblast intersection_of: part_of UBERON:0002048 ! lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-03-16T16:15:39Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-03-16T16:15:39Z" xsd:dateTime [Term] id: CL:4033027 @@ -36608,9 +36645,9 @@ synonym: "DB1 bipolar cell" RELATED OMO:0003000 [PMID:22006647] synonym: "DB1 cell" RELATED OMO:0003000 [PMID:32032773] synonym: "Diffuse Bipolar Cell Type DB1" EXACT [PMID:22006647] is_a: CL:0000750 ! OFF-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T10:48:29Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T10:48:29Z" xsd:dateTime [Term] id: CL:4033028 @@ -36620,9 +36657,9 @@ comment: In primates, a diffuse bipolar 2 cell makes an average of 133 ribbon sy subset: human_reference_atlas synonym: "DB2 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T10:49:07Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T10:49:07Z" xsd:dateTime [Term] id: CL:4033029 @@ -36633,9 +36670,9 @@ subset: human_reference_atlas synonym: "DB3 cell" RELATED OMO:0003000 [DOI:10.3389/fnana.2015.00122] synonym: "DB3a cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T10:53:33Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T10:53:33Z" xsd:dateTime [Term] id: CL:4033030 @@ -36645,9 +36682,9 @@ comment: In humans, a DB3b cell is CD15 positive. A DB3b cell might make sparse subset: human_reference_atlas synonym: "DB3b cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T10:53:42Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T10:53:42Z" xsd:dateTime [Term] id: CL:4033031 @@ -36656,9 +36693,9 @@ def: "An ON diffuse bipolar cell that predominantly connects to ON parasol cells subset: human_reference_atlas synonym: "DB4 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T09:51:10Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T09:51:10Z" xsd:dateTime [Term] id: CL:4033032 @@ -36667,9 +36704,9 @@ def: "An ON diffuse bipolar cell that has a large dendritic field and large axon subset: human_reference_atlas synonym: "DB6 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T09:51:22Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T09:51:22Z" xsd:dateTime [Term] id: CL:4033033 @@ -36678,9 +36715,9 @@ def: "An OFF bipolar cell with a small dendritic tree that provides most of the subset: human_reference_atlas synonym: "FMB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T10:54:00Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T10:54:00Z" xsd:dateTime [Term] id: CL:4033034 @@ -36689,9 +36726,9 @@ def: "An ON bipolar cell with a small dendritic tree that forms most of the cent subset: human_reference_atlas synonym: "IMB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T09:51:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T09:51:44Z" xsd:dateTime [Term] id: CL:4033035 @@ -36700,8 +36737,8 @@ def: "An ON bipolar cell that has large dendritic and axonal fields." [PMID:3203 comment: A giant bipolar cell is usually monostratified, although, very rarely, it can be bistratified. {xref="PMID:32032773"} synonym: "GB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T09:54:15Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T09:54:15Z" xsd:dateTime [Term] id: CL:4033036 @@ -36710,9 +36747,9 @@ def: "An OFF bipolar cell that is fovea-specific and expresses FEZF1, NXPH1 and is_a: BFO:0000002 is_a: CL:0000750 ! OFF-bipolar cell relationship: part_of UBERON:0001786 ! fovea centralis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-04T10:54:15Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9443 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-04T10:54:15Z" xsd:dateTime [Term] id: CL:4033037 @@ -36725,8 +36762,8 @@ intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree intersection_of: part_of UBERON:8410077 ! airway submucosal gland relationship: part_of UBERON:8410077 ! airway submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-04-20T10:55:50Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-04-20T10:55:50Z" xsd:dateTime [Term] id: CL:4033038 @@ -36737,10 +36774,10 @@ synonym: "lung CD4-positive TRM" RELATED OMO:0003000 [PMID:31265968] synonym: "lung resident memory CD4 T cell" EXACT [PMID:24064670] is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell relationship: part_of UBERON:0002048 ! lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-04-27T10:15:45Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-04-27T10:15:45Z" xsd:dateTime [Term] id: CL:4033039 @@ -36751,10 +36788,10 @@ subset: human_reference_atlas synonym: "lung CD8-positive TRM" RELATED OMO:0003000 [PMID:31265968] is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell relationship: part_of UBERON:0002048 ! lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-04-27T10:16:07Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-04-27T10:16:07Z" xsd:dateTime [Term] id: CL:4033040 @@ -36767,9 +36804,9 @@ is_a: CL:4033039 ! lung resident memory CD8-positive, alpha-beta T cell intersection_of: CL:4033039 ! lung resident memory CD8-positive, alpha-beta T cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E relationship: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-05-24T12:23:35Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-05-24T12:23:35Z" xsd:dateTime [Term] id: CL:4033041 @@ -36779,10 +36816,10 @@ subset: human_reference_atlas synonym: "alveolar macrophage CCL3-positive" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage relationship: RO:0002292 PR:000002123 ! expresses C-C motif chemokine 3 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-06-15T12:53:08Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-06-15T12:53:08Z" xsd:dateTime [Term] id: CL:4033042 @@ -36792,10 +36829,10 @@ subset: human_reference_atlas synonym: "alveolar macrophage metallothionein-positive" EXACT [PMID:37291214] synonym: "alveolar macrophage MT-positive" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-06-15T12:55:34Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-06-15T12:55:34Z" xsd:dateTime [Term] id: CL:4033043 @@ -36807,10 +36844,10 @@ is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:0002320 ! connective tissue cell is_a: CL:1001603 ! lung macrophage relationship: part_of UBERON:0000114 ! lung connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-06-15T12:58:11Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-06-15T12:58:11Z" xsd:dateTime [Term] id: CL:4033044 @@ -36819,11 +36856,10 @@ def: "An epithelial cell part of respiratory tract epithelium that is a precurso comment: In humans, deuterosomal cells have been noted to have enriched expression of the following: PLK4, FOXJ1, DEUP1, FOXN4, YPEL1, HES6 and CDC20B. Deuterosomal cells were termed after deuterosomes, the platforms of active centriole amplification. {xref="PMID:31558434", xref="PMID:36883528", xref="PMID:331922198"} subset: human_reference_atlas is_a: CL:0002368 ! respiratory epithelial cell -relationship: part_of UBERON:0004802 ! respiratory tract epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-06-20T10:27:17Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-06-20T10:27:17Z" xsd:dateTime [Term] id: CL:4033045 @@ -36833,10 +36869,10 @@ subset: human_reference_atlas synonym: "lung mDC" RELATED OMO:0003000 [PMID:34516781] synonym: "lung mDCs" RELATED OMO:0003004 [PMID:34516781] is_a: CL:0000451 ! dendritic cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-06-21T10:04:46Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-06-21T10:04:46Z" xsd:dateTime [Term] id: CL:4033046 @@ -36849,8 +36885,8 @@ is_a: CL:4023032 ! ON retinal ganglion cell is_a: CL:4023188 ! midget ganglion cell of retina intersection_of: CL:4023032 ! ON retinal ganglion cell intersection_of: CL:4023188 ! midget ganglion cell of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-08T09:40:08Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-08T09:40:08Z" xsd:dateTime [Term] id: CL:4033047 @@ -36863,8 +36899,8 @@ is_a: CL:4023033 ! OFF retinal ganglion cell is_a: CL:4023188 ! midget ganglion cell of retina intersection_of: CL:4023033 ! OFF retinal ganglion cell intersection_of: CL:4023188 ! midget ganglion cell of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-08T11:05:37Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-08T11:05:37Z" xsd:dateTime [Term] id: CL:4033048 @@ -36876,12 +36912,11 @@ synonym: "respiratory parabasal cell" EXACT [PMID:25564622] synonym: "respiratory suprabasal progenitor cell" EXACT [PMID:25658372] is_a: CL:0002368 ! respiratory epithelial cell is_a: CL:0011026 ! progenitor cell -relationship: part_of UBERON:0004802 ! respiratory tract epithelium relationship: RO:0002202 CL:0002633 ! develops from respiratory basal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-06-20T10:44:30Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-06-20T10:44:30Z" xsd:dateTime [Term] id: CL:4033049 @@ -36894,8 +36929,8 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000209 ! taste receptor cell intersection_of: part_of UBERON:0014451 ! tongue taste bud relationship: part_of UBERON:0014451 ! tongue taste bud -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-05-03T07:59:58Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-05-03T07:59:58Z" xsd:dateTime [Term] id: CL:4033050 @@ -36907,8 +36942,8 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0160043 ! catecholamine secretion, neurotransmission relationship: capable_of GO:0160043 ! catecholamine secretion, neurotransmission -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-05-18T12:07:45Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-05-18T12:07:45Z" xsd:dateTime [Term] id: CL:4033051 @@ -36921,8 +36956,8 @@ is_a: CL:4023033 ! OFF retinal ganglion cell is_a: CL:4023189 ! parasol ganglion cell of retina intersection_of: CL:4023033 ! OFF retinal ganglion cell intersection_of: CL:4023189 ! parasol ganglion cell of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-08T12:34:57Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-08T12:34:57Z" xsd:dateTime [Term] id: CL:4033052 @@ -36935,8 +36970,8 @@ is_a: CL:4023032 ! ON retinal ganglion cell is_a: CL:4023189 ! parasol ganglion cell of retina intersection_of: CL:4023032 ! ON retinal ganglion cell intersection_of: CL:4023189 ! parasol ganglion cell of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-08T12:39:35Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-08T12:39:35Z" xsd:dateTime [Term] id: CL:4033053 @@ -36949,8 +36984,8 @@ synonym: "small bistratified cell" EXACT [PMID:32032773] synonym: "small bistratified cell, blue-ON/yellow-OFF ganglion cell" EXACT [doi:10.1002/cne.22183] is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0002100 UBERON:0001792 ! has soma location ganglionic layer of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-08T12:43:56Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-08T12:43:56Z" xsd:dateTime [Term] id: CL:4033054 @@ -36960,8 +36995,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature relationship: adjacent_to UBERON:0002049 ! vasculature -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-22T13:40:28Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: CL:4033055 @@ -36974,10 +37009,10 @@ intersection_of: part_of UBERON:8410077 ! airway submucosal gland intersection_of: part_of UBERON:8600014 ! submucosal gland ciliated duct relationship: part_of UBERON:8410077 ! airway submucosal gland relationship: part_of UBERON:8600014 ! submucosal gland ciliated duct -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-09-08T10:32:27Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-09-08T10:32:27Z" xsd:dateTime [Term] id: CL:4033056 @@ -36986,9 +37021,9 @@ def: "A differentiated flat keratinocyte that is part of a nail plate. An onycho subset: human_reference_atlas is_a: CL:0000312 ! keratinocyte relationship: part_of UBERON:0008198 ! nail plate -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-10-03T12:49:46Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-10-03T12:49:46Z" xsd:dateTime [Term] id: CL:4033057 @@ -37007,9 +37042,9 @@ synonym: "luminal secretory cell" BROAD [PMID:37380767] synonym: "LumSec" RELATED OMO:0003000 [PMID:37380767] is_a: CL:0002326 ! luminal epithelial cell of mammary gland is_a: CL:0011026 ! progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4969-670X -property_value: http://purl.org/dc/terms/date "2023-10-13T13:02:55Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0003-4969-670X +property_value: terms:date "2023-10-13T13:02:55Z" xsd:dateTime [Term] id: CL:4033058 @@ -37029,9 +37064,9 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:0000512 ! paracrine cell is_a: CL:0002326 ! luminal epithelial cell of mammary gland relationship: RO:0002104 PR:000007204 ! has plasma membrane part estrogen receptor -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4969-670X -property_value: http://purl.org/dc/terms/date "2023-10-16T08:30:25Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0003-4969-670X +property_value: terms:date "2023-10-16T08:30:25Z" xsd:dateTime [Term] id: CL:4033059 @@ -37042,9 +37077,9 @@ synonym: "LMC major luminal cluster 1" RELATED [PMID:35091553] synonym: "luminal cluster 1 cell" BROAD [PMID:34097179] synonym: "progenitor MEC" RELATED OMO:0003000 [PMID:35091553] is_a: CL:0002325 ! lactocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4361-817X -property_value: http://purl.org/dc/terms/date "2023-10-16T13:15:36Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0003-4361-817X +property_value: terms:date "2023-10-16T13:15:36Z" xsd:dateTime [Term] id: CL:4033060 @@ -37054,20 +37089,20 @@ synonym: "LC2" RELATED OMO:0003000 [PMID:35091553] synonym: "LMC major luminal cluster 2" RELATED [PMID:35091553] synonym: "luminal cluster 2 cell" BROAD [PMID:35377806] is_a: CL:0002325 ! lactocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4361-817X -property_value: http://purl.org/dc/terms/date "2023-10-16T13:15:55Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0003-4361-817X +property_value: terms:date "2023-10-16T13:15:55Z" xsd:dateTime [Term] id: CL:4033061 name: endothelial cell of central vein of liver def: "An endothelial cell that is part of a central vein of liver." [PMID:28287163] synonym: "endothelial cell of central vein" BROAD [PMID:28287163] -is_a: CL:0000115 ! endothelial cell +is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0006841 ! central vein of liver relationship: part_of UBERON:0006841 ! central vein of liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033062 @@ -37081,9 +37116,9 @@ synonym: "invasive interstitial extravillous trophoblast cell" EXACT [doi:10.100 is_a: BFO:0000002 is_a: CL:0000351 ! trophoblast cell relationship: RO:0002202 CL:0008036 ! develops from extravillous trophoblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2024-01-08T15:43:15Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-01-08T15:43:15Z" xsd:dateTime [Term] id: CL:4033063 @@ -37097,9 +37132,9 @@ synonym: "endovascular trophoblast" RELATED [PMID:11337369] is_a: BFO:0000002 is_a: CL:0000351 ! trophoblast cell relationship: RO:0002202 CL:0008036 ! develops from extravillous trophoblast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2024-01-08T15:43:32Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-01-08T15:43:32Z" xsd:dateTime [Term] id: CL:4033064 @@ -37112,9 +37147,9 @@ is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000995 ! uterus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2024-01-08T16:05:09Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-01-08T16:05:09Z" xsd:dateTime [Term] id: CL:4033065 @@ -37126,9 +37161,37 @@ synonym: "preplasmablastic cell" EXACT [PMID:33661294] is_a: CL:0000785 ! mature B cell relationship: RO:0002202 CL:0000788 ! develops from naive B cell relationship: RO:0002203 CL:0000980 ! develops into plasmablast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 -property_value: http://purl.org/dc/terms/date "2024-04-25T09:14:58Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2024-04-25T09:14:58Z" xsd:dateTime + +[Term] +id: CL:4033066 +name: pre-granulosa cell +def: "A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles." [PMID:17639032, PMID:32759216, PMID:33970370, PMID:38178246] +synonym: "ovarian pregranulosa cell" EXACT [PMID:32759216] +synonym: "PG cell" RELATED OMO:0003000 [PMID:32759216] +synonym: "pregranulosa cell" EXACT [PMID:17639032, PMID:32759216] +is_a: CL:0000630 ! supporting cell +relationship: part_of UBERON:0000992 ! ovary +relationship: RO:0002210 CL:0000501 ! directly develops into granulosa cell +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2024-06-07T12:04:57Z" xsd:dateTime + +[Term] +id: CL:4033067 +name: mural granulosa cell +def: "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)." [PMID:27815559, PMID:33970370, PMID:34198768] +synonym: "MGC" RELATED OMO:0003000 [doi:10.1530/REP-16-0500] +synonym: "mural GC" RELATED OMO:0003000 [PMID:34198768] +xref: EFO:0005289 +is_a: CL:0002174 ! follicular cell of ovary +is_a: CL:2000064 ! ovarian surface epithelial cell +relationship: RO:0002207 CL:0000501 ! directly develops from granulosa cell +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2024-06-07T12:15:13Z" xsd:dateTime [Term] id: CL:4040000 @@ -37139,8 +37202,8 @@ synonym: "GRP cell" RELATED OMO:0003000 [PMID:11756508] synonym: "tripotential glial-restricted precursor cell" EXACT [PMID:11921204] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-04-03T14:54:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-04-03T14:54:32Z" xsd:dateTime [Term] id: CL:4040001 @@ -37148,10 +37211,10 @@ name: chorionic girdle cell def: "A horse-specific, highly invasive trophoblast cell that invades the endometrium where it forms endometrial cups." [PMID:27280409, PMID:35328607] synonym: "equine chorionic girdle cell" EXACT [PMID:35328607] is_a: CL:0011101 ! chorionic trophoblast cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-04-03T15:08:05Z" xsd:dateTime -property_value: note "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup." xsd:string {xref="PMID:27280409"} +property_value: oboInOwl:note "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup." xsd:string {xref="PMID:27280409"} property_value: RO:0002175 NCBITaxon:9789 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-04-03T15:08:05Z" xsd:dateTime [Term] id: CL:4040002 @@ -37164,20 +37227,21 @@ intersection_of: CL:0000125 ! glial cell intersection_of: part_of UBERON:0002005 ! enteric nervous system relationship: part_of UBERON:0002005 ! enteric nervous system relationship: RO:0002292 PR:000007939 ! expresses glial fibrillary acidic protein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-04-03T15:15:40Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-04-03T15:15:40Z" xsd:dateTime [Term] id: CL:4040003 -name: fetal pre-type II pneumocyte +name: fetal pre-type II pulmonary alveolar epithelial cell def: "Precursor of type II pneumocyte. These cells do not have lamellar bodies, which are a marker of type II pneumocyte maturity." [PMID:1316350] synonym: "fetal alveolar pre-type II epithelial cell" EXACT [PMID:9624168] synonym: "fetal pre-type 2 pneumocyte" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "fetal pre-type II alveolar epithelial cell" EXACT [PMID:12114192] -is_a: CL:0000322 ! pneumocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-06-02T09:19:31Z" xsd:dateTime -property_value: note "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)." xsd:string +synonym: "fetal pre-type II pneumocyte" EXACT [] +is_a: CL:0000322 ! pulmonary alveolar epithelial cell +property_value: oboInOwl:note "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)." xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-06-02T09:19:31Z" xsd:dateTime [Term] id: CL:4040004 @@ -37190,8 +37254,8 @@ is_a: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: part_of UBERON:0004088 ! orbital region relationship: part_of UBERON:0004088 ! orbital region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-09-18T10:43:00Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-09-18T10:43:00Z" xsd:dateTime [Term] id: CL:4040005 @@ -37203,8 +37267,8 @@ synonym: "SCAPs" RELATED OMO:0003004 [PMID:30834270] synonym: "stem cells from the apical papilla" BROAD OMO:0003004 [PMID:30834270] is_a: CL:0000134 ! mesenchymal stem cell relationship: part_of UBERON:0003677 ! tooth root -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-11-02T09:44:47Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-11-02T09:44:47Z" xsd:dateTime [Term] id: CL:4040006 @@ -37212,8 +37276,8 @@ name: dermal chromatophore def: "A chromatophore that is part of the dermis." [PMID:28553007] is_a: CL:0000147 ! pigment cell relationship: part_of UBERON:0002067 ! dermis -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2024-03-07T09:37:14Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2024-03-07T09:37:14Z" xsd:dateTime [Term] id: CL:4042001 @@ -37224,8 +37288,8 @@ is_a: CL:0000402 ! CNS interneuron is_a: CL:0011005 ! GABAergic interneuron relationship: RO:0002100 UBERON:0002435 ! has soma location striatum relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-03-05T14:29:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-03-05T14:29:32Z" xsd:dateTime [Term] id: CL:4042002 @@ -37237,8 +37301,8 @@ synonym: "TAC3-positive D1Sh-MSN" RELATED OMO:0003000 [PMID:34727523] synonym: "TAC3-positive MSN" RELATED OMO:0003000 [PMID:34727523] is_a: CL:4030051 ! nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-03-05T13:36:54Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-03-05T13:36:54Z" xsd:dateTime [Term] id: CL:4042003 @@ -37249,8 +37313,8 @@ synonym: "BAM" RELATED OMO:0003000 [PMID:36945367] synonym: "CAM" RELATED OMO:0003000 [PMID:33556248] synonym: "CNS-associated macrophage" RELATED [PMID:37232741] is_a: CL:0000878 ! central nervous system macrophage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-03-26T16:39:56Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-03-26T16:39:56Z" xsd:dateTime [Term] id: CL:4042004 @@ -37261,8 +37325,8 @@ synonym: "epiplexus cpMΦ" RELATED OMO:0003000 [PMID:38347231] synonym: "Kolmer’s cell" EXACT [PMID:31433571] is_a: CL:0000880 ! choroid plexus macrophage relationship: part_of UBERON:0003911 ! choroid plexus epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-03-26T19:14:58Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-03-26T19:14:58Z" xsd:dateTime [Term] id: CL:4042005 @@ -37272,8 +37336,8 @@ synonym: "cpstMΦ" RELATED OMO:0003000 [PMID:37626977] synonym: "stromal cpMΦ" RELATED OMO:0003000 [PMID:37232741, PMID:38347231] is_a: CL:0000880 ! choroid plexus macrophage relationship: part_of UBERON:0005206 ! choroid plexus stroma -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-03-26T19:21:51Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-03-26T19:21:51Z" xsd:dateTime [Term] id: CL:4042006 @@ -37282,8 +37346,8 @@ def: "A border associated macrophage which is part of a dura matter. This macrop synonym: "dmMΦ" RELATED OMO:0003000 [PMID:37232741] is_a: CL:4042003 ! border associated macrophage relationship: part_of UBERON:0002092 ! brain dura mater -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-03-26T19:27:03Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-03-26T19:27:03Z" xsd:dateTime [Term] id: CL:4042007 @@ -37295,8 +37359,8 @@ is_a: CL:0002605 ! astrocyte of the cerebral cortex is_a: CL:0010012 ! cerebral cortex neuron relationship: part_of UBERON:0001950 ! neocortex relationship: RO:0002100 UBERON:0001950 ! has soma location neocortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-04-08T16:01:24Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-08T16:01:24Z" xsd:dateTime [Term] id: CL:4042008 @@ -37308,8 +37372,8 @@ is_a: CL:0000127 ! astrocyte is_a: CL:2000029 ! central nervous system neuron relationship: part_of UBERON:0002316 ! white matter relationship: RO:0002100 UBERON:0002316 ! has soma location white matter -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-04-08T16:29:28Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-08T16:29:28Z" xsd:dateTime [Term] id: CL:4042009 @@ -37321,16 +37385,16 @@ is_a: CL:0002605 ! astrocyte of the cerebral cortex is_a: CL:0010012 ! cerebral cortex neuron relationship: part_of UBERON:0001950 ! neocortex relationship: RO:0002100 UBERON:0001950 ! has soma location neocortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-04-08T16:33:45Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-08T16:33:45Z" xsd:dateTime [Term] id: CL:4042010 name: pial interlaminar astrocyte def: "An interlaminar astrocyte whose soma is part of the first layer of a neocortex and is in contact with a pia surface." [PMID:32930323, PMID:37139179] is_a: CL:4042009 ! interlaminar astrocyte -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-04-08T16:37:57Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-08T16:37:57Z" xsd:dateTime [Term] id: CL:4042011 @@ -37338,8 +37402,29 @@ name: subpial interlaminar astrocyte def: "An interlaminar astrocyte type whose soma is part of the upper first layer of the neocortex and its processes extend to a pia surface." [PMID:32930323, PMID:37139179] is_a: CL:4042009 ! interlaminar astrocyte relationship: RO:0002170 UBERON:0002361 ! connected to pia mater -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 -property_value: http://purl.org/dc/terms/date "2024-04-08T16:39:09Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-08T16:39:09Z" xsd:dateTime + +[Term] +id: CL:4042012 +name: L2 marginal neuron +def: "An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1." [PMID:29311847, PMID:32108571] +synonym: "L2MN" RELATED OMO:0003000 [PMID:29311847, PMID:32108571] +synonym: "layer 2 marginal neuron" EXACT [PMID:32108571] +is_a: CL:4030060 ! L2 intratelencephalic projecting glutamatergic neuron +property_value: IAO:0000028 "L2MN" xsd:string +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-23T09:31:39Z" xsd:dateTime + +[Term] +id: CL:4042013 +name: Lamp5 Lhx6 neuron +def: "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:34004146, PMID:36007006, PMID:37824655, PMID:37824669] +synonym: "Ivy cell" EXACT [PMID:36007006] +synonym: "Lamp5-Lhx6 type" EXACT [PMID:30382198] +is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-04-23T09:37:55Z" xsd:dateTime [Term] id: CP:0000000 @@ -37441,6 +37526,23 @@ intersection_of: GO:0098813 ! nuclear chromosome segregation intersection_of: part_of GO:0140014 ! mitotic nuclear division relationship: part_of GO:0140014 ! mitotic nuclear division +[Term] +id: GO:0000105 +name: L-histidine biosynthetic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators] +synonym: "histidine anabolism" EXACT [] +synonym: "histidine biosynthesis" EXACT [] +synonym: "histidine biosynthetic process" BROAD [] +synonym: "histidine formation" EXACT [] +synonym: "histidine synthesis" EXACT [] +xref: MetaCyc:HISTSYN-PWY +is_a: GO:0006547 ! L-histidine metabolic process +is_a: GO:0009058 ! biosynthetic process +intersection_of: GO:0009058 ! biosynthetic process +intersection_of: has_primary_output CHEBI:57595 +relationship: has_primary_output CHEBI:57595 + [Term] id: GO:0000122 name: negative regulation of transcription by RNA polymerase II @@ -37545,7 +37647,7 @@ id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -45970,7 +46072,7 @@ relationship: part_of GO:0003091 ! renal water homeostasis id: GO:0003104 name: positive regulation of glomerular filtration namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule." [GOC:mtg_cardio] +def: "Any process that activates or increases the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process whereby blood is filtered by the glomerulus into the renal tubule." [GOC:mtg_cardio] is_a: GO:0003093 ! regulation of glomerular filtration is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation @@ -45981,7 +46083,7 @@ relationship: positively_regulates GO:0003094 ! glomerular filtration id: GO:0003105 name: negative regulation of glomerular filtration namespace: biological_process -def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule." [GOC:mtg_cardio] +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process whereby blood is filtered by the glomerulus into the renal tubule." [GOC:mtg_cardio] is_a: GO:0003093 ! regulation of glomerular filtration is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation @@ -48055,9 +48157,8 @@ name: nuclear steroid receptor activity namespace: molecular_function def: "Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function." [GOC:signaling, PMID:14708019] synonym: "steroid hormone receptor activity" BROAD [] -is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific -is_a: GO:0038023 ! signaling receptor activity -relationship: part_of GO:0043401 ! steroid hormone mediated signaling pathway +is_a: GO:0004879 ! nuclear receptor activity +relationship: part_of GO:0043401 ! steroid hormone receptor signaling pathway property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26957" xsd:anyURI @@ -48616,6 +48717,51 @@ xref: Reactome:R-HSA-8987255 "IL26:IL10RB:p-TYK2:IL20RA:p-JAK1:STAT1,STAT3 phos is_a: GO:0004713 ! protein tyrosine kinase activity is_a: GO:0019199 ! transmembrane receptor protein kinase activity +[Term] +id: GO:0004879 +name: nuclear receptor activity +namespace: molecular_function +alt_id: GO:0003708 +alt_id: GO:0004880 +alt_id: GO:0004882 +alt_id: GO:0004884 +alt_id: GO:0004886 +alt_id: GO:0004887 +alt_id: GO:0008434 +alt_id: GO:0038050 +alt_id: GO:0038051 +alt_id: GO:0038052 +def: "A DNA-binding transcription factor activity regulated by binding to a ligand that modulates the transcription of specific gene sets transcribed by RNA polymerase II. Nuclear receptor ligands are usually lipid-based (such as a steroid hormone) and the binding of the ligand to its receptor often occurs in the cytosol, which leads to its translocation to the nucleus." [GOC:txnOH-2018, PMID:23457262] +comment: Usage guidance: Nuclear receptors are a protein family defined by the presence of a C4-type zinc finger DNA-binding domain and a ligand binding domain. For nuclear receptors, the DNA binding motif is most often referred to as a response element. GO:0004879 is intended for annotation of nuclear receptors that regulate transcription by binding directly to DNA. When the nuclear receptor functions by binding to other transcription factors or transcription factor complexes, consider instead annotating to 'GO:0030374 ; nuclear receptor transcription coactivator activity' or GO:0140536 ; nuclear corepressor activity. +synonym: "1,25-(OH)2D3 receptor activity" NARROW [Wikipedia:Calcitriol] +synonym: "9-cis retinoic acid receptor activity" NARROW [] +synonym: "androgen receptor activity" NARROW [] +synonym: "calcitriol receptor activity" NARROW [] +synonym: "ecdysteroid hormone receptor activity" NARROW [] +synonym: "estrogen nuclear receptor activity" NARROW [GOC:bf] +synonym: "glucocorticoid receptor activity" NARROW [GOC:bf] +synonym: "juvenile hormone receptor activity" NARROW [] +synonym: "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] +synonym: "ligand-dependent nuclear receptor activity" RELATED [GOC:bf] +synonym: "ligand-dependent transcription factor activity" RELATED [GOC:bf] +synonym: "nuclear hormone receptor" NARROW [] +synonym: "retinoic acid receptor activity" NARROW [] +synonym: "retinoid-X receptor activity" NARROW [GOC:bf] +synonym: "RNA polymerase II transcription factor activity, estrogen-activated sequence-specific DNA binding" NARROW [] +synonym: "RNA polymerase II transcription factor activity, glucocorticoid-activated sequence-specific DNA binding" NARROW [] +synonym: "RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding" EXACT [] +synonym: "RXR" NARROW [] +synonym: "thyroid hormone receptor activity" NARROW [] +synonym: "vitamin A receptor activity" NARROW [] +synonym: "vitamin D receptor activity" NARROW [] +synonym: "vitamin D3 receptor activity" NARROW [GOC:bf, Wikipedia:Calcitriol_receptor] +is_a: GO:0000981 ! DNA-binding transcription factor activity, RNA polymerase II-specific +is_a: GO:0038023 ! signaling receptor activity +is_a: GO:0098531 ! ligand-activated transcription factor activity +relationship: part_of GO:0030522 ! intracellular receptor signaling pathway +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19518" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20253" xsd:anyURI + [Term] id: GO:0004883 name: nuclear glucocorticoid receptor activity @@ -48626,7 +48772,7 @@ is_a: GO:0003707 ! nuclear steroid receptor activity intersection_of: GO:0038023 ! signaling receptor activity intersection_of: has_primary_input CHEBI:24261 relationship: has_primary_input CHEBI:24261 -relationship: part_of GO:0042921 ! intracellular glucocorticoid receptor signaling pathway +relationship: part_of GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway relationship: part_of GO:0043402 ! glucocorticoid mediated signaling pathway property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16717" xsd:anyURI @@ -48679,7 +48825,7 @@ alt_id: GO:0001623 alt_id: GO:0001624 alt_id: GO:0001625 alt_id: GO:0016526 -def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR] +def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, Wikipedia:GPCR] subset: goslim_chembl synonym: "EBV-induced receptor" NARROW [] synonym: "Epstein-Barr Virus-induced receptor activity" NARROW [] @@ -48948,7 +49094,7 @@ id: GO:0005215 name: transporter activity namespace: molecular_function alt_id: GO:0005478 -def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf] +def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells." [GOC:ai, GOC:dgf] comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. subset: gocheck_do_not_annotate subset: goslim_agr @@ -48966,6 +49112,7 @@ subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "carrier" RELATED [] is_a: GO:0003674 ! molecular_function +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27621" xsd:anyURI [Term] id: GO:0005216 @@ -49025,7 +49172,7 @@ name: monoatomic cation channel activity namespace: molecular_function alt_id: GO:0015281 alt_id: GO:0015338 -def: "Enables the energy-independent passage of monoatomic cations across a lipid bilayer down a concentration gradient." [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729] +def: "Enables the energy-independent facilitated diffusion of a monoatomic cation through a transmembrane aqueous pore or channel." [GOC:def, GOC:dph, GOC:mtg_transport, GOC:pr, ISBN:0815340729] synonym: "cation channel activity" BROAD [] synonym: "cation diffusion facilitator activity" EXACT [] synonym: "non-selective cation channel activity" NARROW [] @@ -49049,7 +49196,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0005262 name: calcium channel activity namespace: molecular_function -def: "Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, GOC:pr, ISBN:0815340729] +def: "Enables the energy-independent facilitated diffusion of a calcium ion through a transmembrane aqueous pore or channel." [GOC:mtg_transport, GOC:pr, ISBN:0815340729] xref: Reactome:R-HSA-139854 "IP3R tetramer:I(1,4,5)P3:4xCa2+ transports Ca2+ from platelet dense tubular system to cytosol" xref: Reactome:R-HSA-139855 "P2X1-mediated entry of Ca++ from plasma" xref: Reactome:R-HSA-210420 "Ca2+ influx through voltage gated Ca2+ channels" @@ -49245,7 +49392,6 @@ name: binding namespace: molecular_function def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. -subset: gocheck_do_not_annotate subset: goslim_pir subset: goslim_plant synonym: "ligand" NARROW [] @@ -49348,9 +49494,10 @@ relationship: has_primary_input CHEBI:30616 [Term] id: GO:0005536 -name: glucose binding +name: D-glucose binding namespace: molecular_function -def: "Binding to D- or L-enantiomers of glucose." [GOC:jl] +def: "Binding to D-enantiomers of glucose." [GOC:jl] +synonym: "glucose binding" BROAD [] is_a: BFO:0000003 is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding @@ -49898,7 +50045,7 @@ relationship: part_of GO:0005737 ! cytoplasm id: GO:0005882 name: intermediate filament namespace: cellular_component -def: "A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins." [http://www.cytochemistry.net/Cell-biology/intermediate_filaments.htm, ISBN:0198506732] +def: "A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins." [ISBN:0198506732, PMID:17493611, PMID:17551517, PMID:7979242] synonym: "intermediate filament associated protein" RELATED [] synonym: "type I intermediate filament associated protein" RELATED [] synonym: "type II intermediate filament associated protein" RELATED [] @@ -49983,6 +50130,18 @@ relationship: has_part GO:0032432 ! actin filament bundle relationship: part_of CL:0000066 ! epithelial cell property_value: RO:0002161 NCBITaxon:4751 +[Term] +id: GO:0005903 +name: brush border +namespace: cellular_component +def: "The dense covering of microvilli on the apical surface of an epithelial cell in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell." [GOC:sl, ISBN:0815316194] +subset: goslim_pir +xref: Wikipedia:Brush_border +is_a: GO:0098862 ! cluster of actin-based cell projections +relationship: has_part GO:0005902 ! microvillus +relationship: part_of CL:0000066 ! epithelial cell +property_value: RO:0002161 NCBITaxon:4751 + [Term] id: GO:0005911 name: cell-cell junction @@ -50277,8 +50436,8 @@ subset: goslim_pir synonym: "aldehyde metabolism" EXACT [] synonym: "alkanal metabolic process" EXACT [] synonym: "alkanal metabolism" EXACT [] +is_a: BFO:0000003 is_a: GO:0044237 ! cellular metabolic process -is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:17478 relationship: has_primary_input_or_output CHEBI:17478 @@ -50290,9 +50449,9 @@ namespace: biological_process def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732] subset: goslim_pir synonym: "organic acid metabolism" EXACT [] +is_a: BFO:0000003 is_a: GO:0044237 ! cellular metabolic process is_a: GO:0044281 ! small molecule metabolic process -is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:64709 relationship: has_primary_input_or_output CHEBI:64709 @@ -50608,7 +50767,7 @@ subset: goslim_yeast synonym: "RNA breakdown" EXACT [] synonym: "RNA catabolism" EXACT [] synonym: "RNA degradation" EXACT [] -is_a: GO:0009057 ! macromolecule catabolic process +is_a: GO:0009056 ! catabolic process is_a: GO:0016070 ! RNA metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:33697 @@ -50985,6 +51144,35 @@ intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:57305 relationship: has_primary_input CHEBI:57305 +[Term] +id: GO:0006547 +name: L-histidine metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators] +synonym: "histidine metabolic process" BROAD [] +synonym: "histidine metabolism" EXACT [] +xref: Wikipedia:Histidine +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process +intersection_of: GO:0008152 ! metabolic process +intersection_of: has_primary_input_or_output CHEBI:57595 +relationship: has_primary_input_or_output CHEBI:57595 + +[Term] +id: GO:0006548 +name: L-histidine catabolic process +namespace: biological_process +def: "The chemical reactions and pathways resulting in the breakdown of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators] +synonym: "histidine breakdown" EXACT [] +synonym: "histidine catabolic process" BROAD [] +synonym: "histidine catabolism" EXACT [] +synonym: "histidine degradation" EXACT [] +is_a: GO:0006547 ! L-histidine metabolic process +is_a: GO:0009056 ! catabolic process +intersection_of: GO:0009056 ! catabolic process +intersection_of: has_primary_input CHEBI:57595 +relationship: has_primary_input CHEBI:57595 + [Term] id: GO:0006575 name: cellular modified amino acid metabolic process @@ -51120,8 +51308,8 @@ subset: goslim_prokaryote_ribbon subset: goslim_yeast synonym: "lipid metabolism" EXACT [] xref: Wikipedia:Lipid_metabolism +is_a: BFO:0000003 is_a: GO:0044238 ! primary metabolic process -is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:18059 relationship: has_primary_input_or_output CHEBI:18059 @@ -51166,7 +51354,6 @@ synonym: "steroidogenesis" EXACT [] xref: Wikipedia:Steroid_metabolisms#Steroid_biosynthesis is_a: GO:0008202 ! steroid metabolic process is_a: GO:0008610 ! lipid biosynthetic process -is_a: GO:1901362 ! organic cyclic compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:35341 relationship: has_primary_output CHEBI:35341 @@ -51211,7 +51398,7 @@ relationship: has_primary_output CHEBI:64600 id: GO:0006701 name: progesterone biosynthetic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC:jl, http://www.cogsci.princeton.edu/] +def: "The chemical reactions and pathways resulting in the formation of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC:jl, PMID:14613534] synonym: "progesterone anabolism" EXACT [] synonym: "progesterone biosynthesis" EXACT [] synonym: "progesterone formation" EXACT [] @@ -51271,7 +51458,7 @@ relationship: has_primary_input CHEBI:35341 id: GO:0006709 name: progesterone catabolic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC:jl, http://www.cogsci.princeton.edu/] +def: "The chemical reactions and pathways resulting in the breakdown of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC:jl, PMID:11392024] synonym: "progesterone breakdown" EXACT [] synonym: "progesterone catabolism" EXACT [] synonym: "progesterone degradation" EXACT [] @@ -51660,7 +51847,7 @@ name: exocytosis namespace: biological_process alt_id: GO:0016194 alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] +def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] synonym: "vesicle exocytosis" EXACT [] @@ -53683,7 +53870,7 @@ relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia id: GO:0007566 name: embryo implantation namespace: biological_process -def: "Attachment of the blastocyst to the uterine lining." [GOC:isa_complete, http://www.medterms.com] +def: "Attachment of the blastocyst to the uterine lining." [GOC:isa_complete, PMID:10882512] synonym: "blastocyst implantation" EXACT [] is_a: GO:0022414 ! reproductive process relationship: part_of GO:0007275 ! multicellular organism development @@ -54051,7 +54238,7 @@ id: GO:0008134 name: transcription factor binding namespace: molecular_function def: "Binding to a transcription factor, a protein required to initiate or regulate transcription." [ISBN:0198506732] -comment: Note that this term should not be used for direct annotation. Please consier one of the more specific descendants, GO:0140297 ; DNA-binding transcription factor binding, GO:0140296 ; general transcription initiation factor binding or GO:0001221 ; transcription coregulator binding. +comment: Note that this term should not be used for direct annotation. Please consider one of the more specific descendants, GO:0140297 ; DNA-binding transcription factor binding, GO:0140296 ; general transcription initiation factor binding or GO:0001221 ; transcription coregulator binding. subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_chembl @@ -54146,7 +54333,6 @@ def: "The chemical reactions and pathways involving steroids, compounds with a 1 synonym: "steroid metabolism" EXACT [] xref: Wikipedia:Steroid_metabolism is_a: GO:0006629 ! lipid metabolic process -is_a: GO:1901360 ! organic cyclic compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:35341 relationship: has_primary_input_or_output CHEBI:35341 @@ -54451,7 +54637,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0008328 name: ionotropic glutamate receptor complex namespace: cellular_component -def: "A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex." [http://www.bris.ac.uk/Depts/Synaptic/info/glutamate.html] +def: "A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex." [PMID:20716669, PMID:34753794] is_a: GO:0034702 ! monoatomic ion channel complex is_a: GO:0098878 ! neurotransmitter receptor complex intersection_of: GO:0032991 ! protein-containing complex @@ -54572,13 +54758,13 @@ relationship: has_primary_input CHEBI:16796 [Term] id: GO:0008519 -name: ammonium transmembrane transporter activity +name: ammonium channel activity namespace: molecular_function alt_id: GO:0015251 alt_id: GO:0051739 -def: "Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." [PMID:17710640] -synonym: "ammonia transmembrane transporter activity" RELATED [] -synonym: "ammonium channel activity" RELATED [] +def: "Enables the energy-independent facilitated diffusion of ammonium through a transmembrane aqueous pore or channel." [PMID:17710640] +synonym: "ammonia transmembrane transporter activity" BROAD [] +synonym: "ammonium transmembrane transporter activity" BROAD [] xref: MetaCyc:RXN-9615 xref: Reactome:R-HSA-444393 "RhCG mediates ammonium influx into kidney collecting duct cells" xref: Reactome:R-HSA-444416 "RHAG transports NH4+ from cytosol to extracellular region (red blood cells)" @@ -54587,6 +54773,7 @@ xref: Reactome:R-HSA-446277 "RhCG mediates ammonium efflux out of kidney collect xref: Reactome:R-HSA-446278 "RhBG mediates ammonium influx into kidney collecting duct cells" xref: Reactome:R-HSA-5623051 "Defective RHAG does not transport NH4+ from cytosol to extracellular region (rbc)" xref: RHEA:28747 +xref: TC:1.A.11 is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: GO:0022857 ! transmembrane transporter activity @@ -54595,6 +54782,7 @@ relationship: has_participant CHEBI:28938 relationship: has_primary_input CHEBI:28938 relationship: part_of GO:0072488 ! ammonium transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23129" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI [Term] @@ -54679,7 +54867,7 @@ synonym: "lipid formation" EXACT [] synonym: "lipid synthesis" EXACT [] synonym: "lipogenesis" EXACT [GOC:sl] is_a: GO:0006629 ! lipid metabolic process -is_a: GO:1901576 ! organic substance biosynthetic process +is_a: GO:0009058 ! biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:18059 relationship: has_primary_output CHEBI:18059 @@ -54821,7 +55009,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33694 relationship: has_primary_output CHEBI:33694 @@ -55104,7 +55291,6 @@ def: "Any process that results in a change in state or activity of a cell or an synonym: "response to water stimulus" EXACT [GOC:dos] is_a: GO:0001101 ! response to acid chemical is_a: GO:0009628 ! response to abiotic stimulus -is_a: GO:0010035 ! response to inorganic substance is_a: GO:1901700 ! response to oxygen-containing compound intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:15377 @@ -55437,7 +55623,6 @@ def: "Any process that results in a change in state or activity of a cell or an synonym: "growth regulator" RELATED [] synonym: "response to hormone stimulus" EXACT [GOC:dos] is_a: GO:0009719 ! response to endogenous stimulus -is_a: GO:0010033 ! response to organic substance property_value: RO:0002161 NCBITaxon:4751 property_value: RO:0002161 NCBITaxon:4890 @@ -55930,31 +56115,6 @@ is_a: GO:0070192 ! chromosome organization involved in meiotic cell cycle intersection_of: GO:0030261 ! chromosome condensation intersection_of: part_of GO:0051321 ! meiotic cell cycle -[Term] -id: GO:0010033 -name: response to organic substance -namespace: biological_process -alt_id: GO:1990367 -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." [GOC:sm, PMID:23356676] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "process resulting in tolerance to organic substance" NARROW [] -is_a: GO:0042221 ! response to chemical -intersection_of: GO:0042221 ! response to chemical -intersection_of: has_primary_input CHEBI:50860 -relationship: has_primary_input CHEBI:50860 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI - -[Term] -id: GO:0010035 -name: response to inorganic substance -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus." [GOC:sm] -is_a: GO:0042221 ! response to chemical -intersection_of: GO:0050896 ! response to stimulus -intersection_of: has_primary_input CHEBI:24835 -relationship: has_primary_input CHEBI:24835 - [Term] id: GO:0010039 name: response to iron ion @@ -56396,7 +56556,7 @@ id: GO:0010594 name: regulation of endothelial cell migration namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:BHF, GOC:dph, GOC:tb] -is_a: GO:0010632 ! regulation of epithelial cell migration +is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0043542 ! endothelial cell migration relationship: regulates GO:0043542 ! endothelial cell migration @@ -56407,7 +56567,7 @@ name: positive regulation of endothelial cell migration namespace: biological_process def: "Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0010594 ! regulation of endothelial cell migration -is_a: GO:0010634 ! positive regulation of epithelial cell migration +is_a: GO:0030335 ! positive regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0043542 ! endothelial cell migration relationship: positively_regulates GO:0043542 ! endothelial cell migration @@ -56418,7 +56578,7 @@ name: negative regulation of endothelial cell migration namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0010594 ! regulation of endothelial cell migration -is_a: GO:0010633 ! negative regulation of epithelial cell migration +is_a: GO:0030336 ! negative regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0043542 ! endothelial cell migration relationship: negatively_regulates GO:0043542 ! endothelial cell migration @@ -57963,7 +58123,7 @@ relationship: results_in_formation_of UBERON:0002328 ! notochord id: GO:0014029 name: neural crest formation namespace: biological_process -def: "The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." [GOC:dh, GOC:ef] +def: "The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds." [GOC:dh, GOC:ef] is_a: GO:0001837 ! epithelial to mesenchymal transition is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis @@ -58366,18 +58526,6 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001820 ! serotonin secretion relationship: positively_regulates GO:0001820 ! serotonin secretion -[Term] -id: GO:0014070 -name: response to organic cyclic compound -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." [GOC:ef] -synonym: "response to organic cyclic substance" EXACT [GOC:mah] -is_a: BFO:0000003 -is_a: GO:0050896 ! response to stimulus -intersection_of: GO:0050896 ! response to stimulus -intersection_of: has_primary_input CHEBI:33832 -relationship: has_primary_input CHEBI:33832 - [Term] id: GO:0014075 name: response to amine @@ -58761,7 +58909,7 @@ is_a: GO:0014819 ! regulation of skeletal muscle contraction id: GO:0014853 name: regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction namespace: biological_process -def: "Any process, involved in skeletal muscle contraction, that modulates the establishment or extent of the excitatory postsynaptic potential (EPSP). Excitatory postsynaptic potential (EPSP) is a temporay increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." [GOC:ef, GOC:mtg_muscle] +def: "Any process, involved in skeletal muscle contraction, that modulates the establishment or extent of the excitatory postsynaptic potential (EPSP). Excitatory postsynaptic potential (EPSP) is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." [GOC:ef, GOC:mtg_muscle] synonym: "regulation of excitatory post-synaptic membrane potential involved in skeletal muscle contraction" EXACT [] is_a: GO:0098815 ! modulation of excitatory postsynaptic potential intersection_of: GO:0098815 ! modulation of excitatory postsynaptic potential @@ -59053,8 +59201,8 @@ subset: goslim_chembl subset: goslim_pir subset: goslim_yeast synonym: "enzyme transport" NARROW [] +is_a: GO:0006810 ! transport is_a: GO:0045184 ! establishment of protein localization -is_a: GO:0071702 ! organic substance transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input PR:000000001 ! protein @@ -59321,7 +59469,7 @@ relationship: part_of GO:0015866 ! ADP transport id: GO:0015250 name: water channel activity namespace: molecular_function -def: "Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [GOC:mtg_transport, ISBN:0815340729] +def: "Enables the energy-independent facilitated diffusion of water through a transmembrane aqueous pore or channel." [GOC:mtg_transport, ISBN:0815340729] synonym: "aquaporin" NARROW [] xref: MetaCyc:TRANS-RXN-145 xref: Reactome:R-HSA-432010 "Aquaporin-1 passively transports water into cell" @@ -59361,7 +59509,7 @@ namespace: molecular_function alt_id: GO:0015249 alt_id: GO:0015268 alt_id: GO:0022838 -def: "Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729] +def: "Enables the energy-independent facilitated diffusion of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729] synonym: "alpha-type channel activity" RELATED [] synonym: "channel-forming toxin activity" RELATED [] synonym: "channel/pore class transporter activity" EXACT [] @@ -59392,20 +59540,6 @@ intersection_of: GO:0022836 ! gated channel activity intersection_of: has_primary_input CHEBI:24867 intersection_of: has_small_molecule_activator CHEBI:24431 -[Term] -id: GO:0015318 -name: inorganic molecular entity transmembrane transporter activity -namespace: molecular_function -def: "Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon." [GOC:mtg_transport, ISBN:0815340729] -subset: gocheck_do_not_annotate -synonym: "inorganic solute uptake transmembrane transporter activity" EXACT [] -synonym: "inorganic uptake permease activity" EXACT [] -is_a: GO:0022857 ! transmembrane transporter activity -intersection_of: GO:0022857 ! transmembrane transporter activity -intersection_of: has_primary_input CHEBI:24835 -relationship: has_primary_input CHEBI:24835 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14372" xsd:anyURI - [Term] id: GO:0015464 name: acetylcholine receptor activity @@ -59576,7 +59710,6 @@ namespace: biological_process def: "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir is_a: GO:0042886 ! amide transport -is_a: GO:0071702 ! organic substance transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:60466 relationship: has_primary_input CHEBI:60466 @@ -59612,7 +59745,8 @@ name: organic hydroxy compound transport namespace: biological_process def: "The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom." [GOC:ai] synonym: "organic alcohol transport" EXACT [] -is_a: GO:0071702 ! organic substance transport +is_a: BFO:0000003 +is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:33822 relationship: has_primary_input CHEBI:33822 @@ -59913,7 +60047,6 @@ synonym: "organic acid synthesis" EXACT [] is_a: GO:0006082 ! organic acid metabolic process is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0044283 ! small molecule biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:64709 relationship: has_primary_output CHEBI:64709 @@ -60539,7 +60672,6 @@ synonym: "hydroxybenzene metabolic process" EXACT [] synonym: "hydroxybenzene metabolism" EXACT [] synonym: "phenol-containing compound metabolism" EXACT [] xref: UM-BBD_pathwayID:phe -is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33853 @@ -60706,7 +60838,6 @@ name: response to pheromone namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus." [GOC:jl] synonym: "pheromone response" EXACT [] -is_a: GO:0010033 ! response to organic substance [Term] id: GO:0019318 @@ -61406,7 +61537,7 @@ relationship: results_in_development_of UBERON:0001645 ! trigeminal nerve id: GO:0021561 name: facial nerve development namespace: biological_process -def: "The process whose specific outcome is the progression of the facial nerve over time, from its formation to the mature structure. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives off nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] +def: "The process whose specific outcome is the progression of the facial nerve over time, from its formation to the mature structure. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial ophthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives off nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] synonym: "CN VII development" RELATED [GOC:cls] synonym: "cranial nerve 7 development" EXACT [GOC:cls] synonym: "cranial nerve VII development" EXACT [GOC:cls] @@ -61777,7 +61908,7 @@ relationship: results_in_formation_of UBERON:0002019 ! accessory XI nerve id: GO:0021610 name: facial nerve morphogenesis namespace: biological_process -def: "The process in which the anatomical structure of the facial nerve is generated and organized. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] +def: "The process in which the anatomical structure of the facial nerve is generated and organized. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial ophthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] synonym: "CN VII morphogenesis" RELATED [] is_a: GO:0021602 ! cranial nerve morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis @@ -61789,7 +61920,7 @@ relationship: results_in_morphogenesis_of UBERON:0001647 ! facial nerve id: GO:0021611 name: facial nerve formation namespace: biological_process -def: "The process that gives rise to the facial nerve. This process pertains to the initial formation of a structure from unspecified parts. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] +def: "The process that gives rise to the facial nerve. This process pertains to the initial formation of a structure from unspecified parts. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial ophthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] synonym: "CN VII biosynthesis" RELATED [] synonym: "CN VII formation" RELATED [] is_a: GO:0021603 ! cranial nerve formation @@ -61802,7 +61933,7 @@ relationship: results_in_formation_of UBERON:0001647 ! facial nerve id: GO:0021613 name: facial nerve maturation namespace: biological_process -def: "A developmental process, independent of morphogenetic (shape) change, that is required for the facial nerve to attain its fully functional state. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] +def: "A developmental process, independent of morphogenetic (shape) change, that is required for the facial nerve to attain its fully functional state. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial ophthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] synonym: "CN VII maturation" RELATED [] is_a: GO:0021605 ! cranial nerve maturation intersection_of: GO:0021700 ! developmental maturation @@ -64099,7 +64230,7 @@ relationship: process_has_causal_agent GO:0005884 ! actin filament id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -64114,7 +64245,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -64175,7 +64306,7 @@ intersection_of: results_in_transport_along GO:0005884 ! actin filament id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -64216,7 +64347,7 @@ intersection_of: has_primary_input PR:000009054 ! insulin gene translation produ relationship: has_primary_input PR:000009054 ! insulin gene translation product relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/11255" xsd:anyURI [Term] id: GO:0030097 @@ -64426,7 +64557,7 @@ relationship: has_primary_input CHEBI:37396 id: GO:0030168 name: platelet activation namespace: biological_process -def: "A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug." [http://www.graylab.ac.uk/omd/] +def: "A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug." [PMID:27403440] synonym: "blood coagulation, platelet activation" EXACT [GOC:add, GOC:pde] is_a: BFO:0000003 is_a: GO:0001775 ! cell activation @@ -65246,7 +65377,7 @@ is_a: GO:0014821 ! phasic smooth muscle contraction id: GO:0030435 name: sporulation resulting in formation of a cellular spore namespace: biological_process -def: "The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:mah, GOC:pamgo_curators, ISBN:0072992913] +def: "The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and desiccation resistance, and/or for reproduction." [GOC:mah, GOC:pamgo_curators, ISBN:0072992913] comment: Note that the synonym 'spore differentiation', like the term name and definition, refers to differentiation into a spore rather than any subsequent developmental changes that a spore may undergo. synonym: "cellular spore formation by sporulation" EXACT [GOC:dph, GOC:tb] synonym: "spore biosynthesis" EXACT [] @@ -65356,13 +65487,14 @@ relationship: negatively_regulates GO:0030282 ! bone mineralization [Term] id: GO:0030518 -name: intracellular steroid hormone receptor signaling pathway +name: nuclear receptor-mediated steroid hormone signaling pathway namespace: biological_process -def: "The series of molecular signals initiated by a steroid binding to an intracellular steroid hormone receptor." [GOC:mah, GOC:signaling] +def: "A nuclear receptor-mediated signaling pathway initiated by a steroid binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah, GOC:signaling] +synonym: "intracellular steroid hormone receptor signaling pathway" EXACT [] synonym: "steroid hormone receptor signaling pathway" BROAD [GOC:bf] synonym: "steroid hormone receptor signalling pathway" BROAD [GOC:bf] -is_a: GO:0043401 ! steroid hormone mediated signaling pathway -is_a: GO:0141193 ! nuclear receptor signaling pathway +is_a: GO:0043401 ! steroid hormone receptor signaling pathway +is_a: GO:0141193 ! nuclear receptor-mediated signaling pathway [Term] id: GO:0030522 @@ -65372,7 +65504,7 @@ def: "The series of molecular signals initiated by a ligand binding to a recepto synonym: "intracellular receptor mediated signaling pathway" EXACT [] synonym: "intracellular receptor-mediated signaling pathway" EXACT [] synonym: "intracellular receptor-mediated signalling pathway" EXACT [] -is_a: GO:0007165 ! signal transduction +is_a: GO:0035556 ! intracellular signal transduction [Term] id: GO:0030539 @@ -65818,7 +65950,7 @@ relationship: positively_regulates GO:0042100 ! B cell proliferation id: GO:0030900 name: forebrain development namespace: biological_process -def: "The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=forebrain] +def: "The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." [PMID:4975589, PMID:4992177] synonym: "prosencephalon development" EXACT [] is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development @@ -65830,7 +65962,7 @@ relationship: results_in_development_of UBERON:0001890 ! forebrain id: GO:0030901 name: midbrain development namespace: biological_process -def: "The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=midbrain] +def: "The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)." [PMID:4975589, PMID:4992177] synonym: "mesencephalon development" EXACT [] is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development @@ -65842,7 +65974,7 @@ relationship: results_in_development_of UBERON:0001891 ! midbrain id: GO:0030902 name: hindbrain development namespace: biological_process -def: "The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium)." [http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=hindbrain] +def: "The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium)." [PMID:4975589, PMID:4992177] synonym: "rhombencephalon development" EXACT [] is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development @@ -67315,12 +67447,12 @@ relationship: positively_regulates GO:0006713 ! glucocorticoid catabolic process [Term] id: GO:0031958 -name: intracellular corticosteroid receptor signaling pathway +name: nuclear receptor-mediated corticosteroid signaling pathway namespace: biological_process -def: "The series of molecular signals initiated by corticosteroid binding to its nuclear receptor inside the cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah, PMID:11027914, PMID:12606724] -synonym: "corticosteroid receptor signaling pathway" BROAD [] +def: "A nuclear receptor-mediated signaling pathway initiated by a corticosteroid binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [PMID:11027914, PMID:12606724] synonym: "corticosteroid receptor signalling pathway" BROAD [] -is_a: GO:0030518 ! intracellular steroid hormone receptor signaling pathway +synonym: "intracellular corticosteroid receptor signaling pathway" EXACT [] +is_a: GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway [Term] id: GO:0031965 @@ -70531,6 +70663,7 @@ name: response to insulin namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [GOC:mah, ISBN:0198506732] synonym: "response to insulin stimulus" EXACT [GOC:dos] +is_a: GO:0042221 ! response to chemical is_a: GO:0043434 ! response to peptide hormone intersection_of: GO:0042221 ! response to chemical intersection_of: has_primary_input PR:000009054 ! insulin gene translation product @@ -70551,7 +70684,6 @@ id: GO:0032870 name: cellular response to hormone stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus." [GOC:mah] -is_a: GO:0071310 ! cellular response to organic substance is_a: GO:0071495 ! cellular response to endogenous stimulus [Term] @@ -71622,10 +71754,10 @@ namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] synonym: "regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] synonym: "regulation of steroid hormone receptor signalling pathway" BROAD [] -is_a: GO:0009966 ! regulation of signal transduction +is_a: GO:1902531 ! regulation of intracellular signal transduction intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway -relationship: regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +intersection_of: regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway +relationship: regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway [Term] id: GO:0033144 @@ -71634,11 +71766,11 @@ namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] synonym: "negative regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] synonym: "negative regulation of steroid hormone receptor signalling pathway" BROAD [GOC:bf] -is_a: GO:0009968 ! negative regulation of signal transduction is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:1902532 ! negative regulation of intracellular signal transduction intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway -relationship: negatively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +intersection_of: negatively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway +relationship: negatively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway [Term] id: GO:0033145 @@ -71647,11 +71779,11 @@ namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." [GOC:mah] synonym: "positive regulation of steroid hormone receptor signaling pathway" BROAD [GOC:bf] synonym: "positive regulation of steroid hormone receptor signalling pathway" BROAD [] -is_a: GO:0009967 ! positive regulation of signal transduction is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway +is_a: GO:1902533 ! positive regulation of intracellular signal transduction intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway -relationship: positively_regulates GO:0030518 ! intracellular steroid hormone receptor signaling pathway +intersection_of: positively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway +relationship: positively_regulates GO:0030518 ! nuclear receptor-mediated steroid hormone signaling pathway [Term] id: GO:0033151 @@ -71862,7 +71994,7 @@ relationship: has_primary_input CHEBI:35757 id: GO:0033326 name: cerebrospinal fluid secretion namespace: biological_process -def: "The regulated release of cerebrospinal fluid (CSF) from the choroid plexus of the lateral, third and fourth ventricles. The cerebrospinal fluid is a clear liquid that located within the ventricles, spinal canal, and subarachnoid spaces." [GOC:ln, http://users.ahsc.arizona.edu/davis/csf.htm, PMID:10716451] +def: "The regulated release of cerebrospinal fluid (CSF) from the choroid plexus of the lateral, third and fourth ventricles. The cerebrospinal fluid is a clear liquid that located within the ventricles, spinal canal, and subarachnoid spaces." [GOC:ln, PMID:10716451] synonym: "CSF secretion" EXACT [] is_a: GO:0007589 ! body fluid secretion is_a: GO:0032941 ! secretion by tissue @@ -72341,7 +72473,7 @@ name: response to cytokine namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." [GOC:sl] synonym: "response to cytokine stimulus" EXACT [GOC:dos] -is_a: GO:0010033 ! response to organic substance +is_a: GO:1901652 ! response to peptide [Term] id: GO:0034101 @@ -72592,7 +72724,7 @@ property_value: RO:0002161 NCBITaxon:33083 id: GO:0034295 name: basidiospore formation namespace: biological_process -def: "The process in which spores form outside a specialized end cell known as a basidium. Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to spores that each contain a haploid nucleus that is the product of meiosis. The spores are usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:di, GOC:ds, GOC:mah, GOC:mcc, http://www.gsbs.utmb.edu/microbook/ch073.htm, http://www.ilmyco.gen.chicago.il.us/Terms/basid133.html] +def: "The process in which spores form outside a specialized end cell known as a basidium. Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to spores that each contain a haploid nucleus that is the product of meiosis. The spores are usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In most basidiomycetes there are four sterigmata (and four spores) to a basidium." [GOC:di, GOC:ds, GOC:mah, GOC:mcc, https://en.wikipedia.org/wiki/Basidiospore] comment: Note that basidiospores and basidia are separate biological structures. The basidium is the structure that bear the basidiospores, but the development of the basidium is a different process than the formation of the basidiospores themselves. For this reason, GO:0034295 basidiospore formation and GO:0075313 basidium development are different terms and are not linked. is_a: BFO:0000003 is_a: GO:0043935 ! sexual sporulation resulting in formation of a cellular spore @@ -72604,7 +72736,7 @@ relationship: results_in_formation_of CL:0000615 ! basidiospore id: GO:0034296 name: zygospore formation namespace: biological_process -def: "The process in which zygospores are formed. Zygospores are characteristic of the zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily ornamented as well, with many spines or ridges. It is formed between two specialized organs called suspensors, which are themselves usually heavily ornamented, one from each mating partner. The zygospore forms between them and then breaks away." [GOC:ds, GOC:mah, http://www.ilmyco.gen.chicago.il.us/Terms/zygos581.html] +def: "The process in which zygospores are formed. Zygospores are characteristic of the zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily ornamented as well, with many spines or ridges. It is formed between two specialized organs called suspensors, which are themselves usually heavily ornamented, one from each mating partner. The zygospore forms between them and then breaks away." [GOC:ds, GOC:mah, PMID:21858438] is_a: BFO:0000003 is_a: GO:0043935 ! sexual sporulation resulting in formation of a cellular spore intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis @@ -73579,7 +73711,7 @@ relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda id: GO:0035190 name: syncytial nuclear migration namespace: biological_process -def: "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex." [GOC:bf, ISBN:0879694238, PMID:8314839] +def: "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisions and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex." [GOC:bf, ISBN:0879694238, PMID:8314839] is_a: GO:0007097 ! nuclear migration intersection_of: GO:0007097 ! nuclear migration intersection_of: occurs_in CL:0000228 ! multinucleate cell @@ -73739,7 +73871,7 @@ is_a: GO:0007268 ! chemical synaptic transmission id: GO:0035260 name: internal genitalia morphogenesis namespace: biological_process -def: "The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals." [http://www.ndif.org/Terms/genitalia.html] +def: "The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals." [PMID:24793987, PMID:25247640] is_a: GO:0035112 ! genitalia morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004175 ! internal genitalia @@ -73749,7 +73881,7 @@ relationship: results_in_morphogenesis_of UBERON:0004175 ! internal genitalia id: GO:0035261 name: external genitalia morphogenesis namespace: biological_process -def: "The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals." [http://www.ndif.org/Terms/genitalia.html] +def: "The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals." [PMID:24793987, PMID:25247640] is_a: GO:0035112 ! genitalia morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0004176 ! external genitalia @@ -74348,11 +74480,10 @@ creation_date: 2011-03-11T10:04:12Z id: GO:0035735 name: intraciliary transport involved in cilium assembly namespace: biological_process -def: "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly." [GOC:bf, GOC:cilia, Reactome:R-HSA-5620924.2] +def: "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly." [GOC:bf, GOC:cilia] synonym: "intraciliary transport involved in cilium morphogenesis" RELATED [] synonym: "intraflagellar transport" BROAD [] synonym: "intraflagellar transport involved in cilium morphogenesis" RELATED [] -xref: Reactome:R-HSA-5620924.2 is_a: GO:0042073 ! intraciliary transport intersection_of: GO:0042073 ! intraciliary transport intersection_of: part_of GO:0060271 ! cilium assembly @@ -74714,7 +74845,7 @@ creation_date: 2011-05-06T01:54:35Z id: GO:0035846 name: oviduct epithelium development namespace: biological_process -def: "The progression of the oviduct epithelium over time from its initial formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. The oviduct epithelium is the specialized epithelium that lines the oviduct." [GOC:yaf, http://www.thefreedictionary.com/oviduct] +def: "The progression of the oviduct epithelium over time from its initial formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. The oviduct epithelium is the specialized epithelium that lines the oviduct." [GOC:yaf, PMID:34496237] synonym: "fallopian tube epithelium development" NARROW [GOC:yaf] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0060429 ! epithelium development @@ -74743,7 +74874,7 @@ creation_date: 2011-05-10T10:57:45Z id: GO:0035848 name: oviduct morphogenesis namespace: biological_process -def: "The process in which anatomical structures of the oviduct are generated and organized. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." [GOC:yaf, http://www.thefreedictionary.com/oviduct] +def: "The process in which anatomical structures of the oviduct are generated and organized. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." [GOC:yaf, PMID:22918811] synonym: "fallopian tube morphogenesis" NARROW [GOC:yaf] is_a: GO:0009887 ! animal organ morphogenesis is_a: GO:0035239 ! tube morphogenesis @@ -75289,7 +75420,7 @@ creation_date: 2012-01-26T01:58:10Z id: GO:0036135 name: Schwann cell migration namespace: biological_process -def: "The orderly movement of a Schwann cell from one site to another. A Schwann cell is a glial cell that ensheathes axons of neuron in the peripheral nervous system and is necessary for their maintainance and function." [CL:0002573, PMID:20335460] +def: "The orderly movement of a Schwann cell from one site to another. A Schwann cell is a glial cell that ensheathes axons of neuron in the peripheral nervous system and is necessary for their maintenance and function." [CL:0002573, PMID:20335460] is_a: GO:0008347 ! glial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0002573 ! Schwann cell @@ -76235,7 +76366,7 @@ id: GO:0042073 name: intraciliary transport namespace: biological_process alt_id: GO:0035734 -def: "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374, Reactome:R-HSA-5620924.2] +def: "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "IFT" RELATED [] synonym: "intraflagellar transport" EXACT [] @@ -76263,7 +76394,7 @@ property_value: RO:0002161 NCBITaxon:5782 id: GO:0042074 name: cell migration involved in gastrulation namespace: biological_process -def: "The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression)." [GOC:jl, http://www.cellmigration.org/, ISBN:0878932437] +def: "The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression)." [GOC:jl, PMID:16099638] is_a: GO:0001667 ! ameboidal-type cell migration intersection_of: GO:0016477 ! cell migration intersection_of: part_of GO:0007369 ! gastrulation @@ -76712,9 +76843,9 @@ namespace: biological_process def: "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." [GOC:jl, ISBN:0787650153] subset: goslim_pir synonym: "ketone metabolism" EXACT [] +is_a: BFO:0000003 is_a: GO:0044237 ! cellular metabolic process is_a: GO:0044281 ! small molecule metabolic process -is_a: GO:0071704 ! organic substance metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:17087 relationship: has_primary_input_or_output CHEBI:17087 @@ -76731,7 +76862,6 @@ synonym: "ketone synthesis" EXACT [] is_a: GO:0042180 ! cellular ketone metabolic process is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0044283 ! small molecule biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17087 relationship: has_primary_output CHEBI:17087 @@ -77378,7 +77508,6 @@ synonym: "indole derivative metabolism" NARROW [] synonym: "indole-containing compound metabolism" EXACT [] synonym: "ketole metabolic process" EXACT [] synonym: "ketole metabolism" EXACT [] -is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24828 @@ -77395,8 +77524,8 @@ synonym: "indole-containing compound anabolism" EXACT [] synonym: "indole-containing compound biosynthesis" EXACT [] synonym: "indole-containing compound formation" EXACT [] synonym: "indole-containing compound synthesis" EXACT [] +is_a: GO:0009058 ! biosynthetic process is_a: GO:0042430 ! indole-containing compound metabolic process -is_a: GO:1901362 ! organic cyclic compound biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:24828 relationship: has_primary_output CHEBI:24828 @@ -77471,7 +77600,7 @@ is_a: GO:0042445 ! hormone metabolic process id: GO:0042448 name: progesterone metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC:jl, http://www.cogsci.princeton.edu/] +def: "The chemical reactions and pathways involving progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." [GOC:jl, PMID:11392024] synonym: "progesterone metabolism" EXACT [] is_a: BFO:0000003 is_a: GO:0008152 ! metabolic process @@ -77965,7 +78094,7 @@ is_a: GO:0042611 ! MHC protein complex id: GO:0042629 name: mast cell granule namespace: cellular_component -def: "Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase." [GOC:jl, http://www.ijp-online.com/archives/1969/001/02/r0000-0000tc.htm, PMID:12360215] +def: "Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase." [GOC:jl, PMID:12360215] is_a: GO:0005764 ! lysosome [Term] @@ -78154,7 +78283,7 @@ relationship: results_in_growth_of UBERON:0000459 ! uterine wall id: GO:0042713 name: sperm ejaculation namespace: biological_process -def: "The expulsion of seminal fluid, thick white fluid containing spermatozoa, from the male genital tract." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "The expulsion of seminal fluid, thick white fluid containing spermatozoa, from the male genital tract." [GOC:jl, PMID:26385403] is_a: GO:0048609 ! multicellular organismal reproductive process relationship: part_of GO:0007320 ! insemination @@ -78202,18 +78331,19 @@ relationship: part_of GO:0042886 ! amide transport [Term] id: GO:0042921 -name: intracellular glucocorticoid receptor signaling pathway +name: nuclear receptor-mediated glucocorticoid signaling pathway namespace: biological_process -def: "The series of molecular signals initiated by glucocorticoid binding to its nuclear receptor inside the cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:mah] +def: "A nuclear receptor-mediated signaling pathway initiated by a glucocorticoid binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:mah] synonym: "glucocorticoid receptor signaling pathway" BROAD [] synonym: "glucocorticoid receptor signalling pathway" BROAD [] -is_a: GO:0031958 ! intracellular corticosteroid receptor signaling pathway +synonym: "intracellular glucocorticoid receptor signaling pathway" EXACT [] +is_a: GO:0031958 ! nuclear receptor-mediated corticosteroid signaling pathway [Term] id: GO:0042923 name: neuropeptide binding namespace: molecular_function -def: "Interacting selectively and non-covalently and stoichiometrically with neuropeptides, peptides with direct synaptic effects (peptide neurotransmitters) or indirect modulatory effects on the nervous system (peptide neuromodulators)." [http://www.wormbook.org/chapters/www_neuropeptides/neuropeptides.html] +def: "Interacting selectively and non-covalently and stoichiometrically with neuropeptides, peptides with direct synaptic effects (peptide neurotransmitters) or indirect modulatory effects on the nervous system (peptide neuromodulators)." [PMID:10414961, PMID:38337033] is_a: GO:0042277 ! peptide binding [Term] @@ -78244,7 +78374,7 @@ property_value: RO:0002161 NCBITaxon:4896 id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -78320,7 +78450,7 @@ intersection_of: process_has_causal_agent GO:0031982 ! vesicle id: GO:0043005 name: neuron projection namespace: cellular_component -def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, PMID:3077060] subset: goslim_pir synonym: "nerve fiber" RELATED [GOC:dph] synonym: "neurite" NARROW [] @@ -79986,10 +80116,11 @@ relationship: has_primary_input CHEBI:37396 [Term] id: GO:0043401 -name: steroid hormone mediated signaling pathway +name: steroid hormone receptor signaling pathway namespace: biological_process def: "The series of molecular signals mediated by a steroid hormone binding to a receptor." [PMID:12606724] synonym: "steroid hormone mediated signalling" EXACT [] +synonym: "steroid hormone-mediated signaling pathway" EXACT [] is_a: GO:0009755 ! hormone-mediated signaling pathway relationship: part_of GO:0071383 ! cellular response to steroid hormone stimulus @@ -79999,7 +80130,7 @@ name: glucocorticoid mediated signaling pathway namespace: biological_process def: "The series of molecular signals mediated by the detection of a glucocorticoid hormone." [PMID:15240347] synonym: "glucocorticoid mediated signalling" EXACT [] -is_a: GO:0043401 ! steroid hormone mediated signaling pathway +is_a: GO:0043401 ! steroid hormone receptor signaling pathway relationship: part_of GO:0071385 ! cellular response to glucocorticoid stimulus [Term] @@ -80098,6 +80229,7 @@ namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals." [PMID:11027914, PMID:15134857, Wikipedia:Peptide_hormone] synonym: "response to peptide hormone stimulus" EXACT [GOC:dos] synonym: "response to polypeptide hormone stimulus" EXACT [] +is_a: BFO:0000003 is_a: GO:0009725 ! response to hormone intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:25905 @@ -80320,7 +80452,8 @@ id: GO:0043542 name: endothelial cell migration namespace: biological_process def: "The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." [GOC:go_curators] -is_a: GO:0010631 ! epithelial cell migration +is_a: BFO:0000003 +is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000115 ! endothelial cell relationship: results_in_movement_of CL:0000115 ! endothelial cell @@ -80633,7 +80766,7 @@ creation_date: 2010-09-08T10:01:42Z id: GO:0043934 name: sporulation namespace: biological_process -def: "The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:pamgo_curators] +def: "The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and desiccation resistance, and/or for reproduction." [GOC:pamgo_curators] subset: goslim_metagenomics subset: goslim_yeast xref: Wikipedia:Spore @@ -80643,7 +80776,7 @@ is_a: GO:0032502 ! developmental process id: GO:0043935 name: sexual sporulation resulting in formation of a cellular spore namespace: biological_process -def: "The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." [GOC:pamgo_curators] +def: "The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and desiccation resistance, and/or for reproduction." [GOC:pamgo_curators] is_a: GO:0030435 ! sporulation resulting in formation of a cellular spore is_a: GO:0034293 ! sexual sporulation intersection_of: GO:0030435 ! sporulation resulting in formation of a cellular spore @@ -80903,13 +81036,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -80965,7 +81099,7 @@ is_a: GO:0044237 ! cellular metabolic process id: GO:0044258 name: intestinal lipid catabolic process namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown into fatty acids and monoglycerides of lipids in the small intestine. Lipids are broken down by lipases released by the pancreas." [GOC:jl, http://www.emc.maricopa.edu/] +def: "The chemical reactions and pathways resulting in the breakdown into fatty acids and monoglycerides of lipids in the small intestine. Lipids are broken down by lipases released by the pancreas." [GOC:jl, PMID:7018485] synonym: "intestinal lipid breakdown" EXACT [] synonym: "intestinal lipid catabolism" EXACT [] synonym: "intestinal lipid degradation" EXACT [] @@ -81571,6 +81705,7 @@ is_a: GO:0008104 ! protein localization is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: has_primary_input CHEBI:36080 +relationship: has_primary_input CHEBI:36080 [Term] id: GO:0045185 @@ -85718,7 +85853,6 @@ synonym: "aldehyde formation" EXACT [] synonym: "aldehyde synthesis" EXACT [] is_a: GO:0006081 ! cellular aldehyde metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:17478 relationship: has_primary_output CHEBI:17478 @@ -88103,6 +88237,7 @@ name: response to steroid hormone namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." [GOC:go_curators] synonym: "response to steroid hormone stimulus" EXACT [GOC:dos] +is_a: BFO:0000003 is_a: GO:0009725 ! response to hormone intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:26764 @@ -91889,7 +92024,7 @@ is_a: GO:0050952 ! sensory perception of electrical stimulus id: GO:0050957 name: equilibrioception namespace: biological_process -def: "The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion." [http://www.medterms.com] +def: "The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion." [PMID:29303967] synonym: "sensory perception of orientation with respect to gravity" EXACT [] xref: Wikipedia:Equilibrioception is_a: GO:0007600 ! sensory perception @@ -92632,7 +92767,7 @@ id: GO:0051132 name: NK T cell activation namespace: biological_process def: "The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [ISBN:0781735149, PMID:12154375, PMID:9133426] -comment: Note that NK T cells are a distinct lineage of T cells expressing natural killer cell markers and having T cell receptors characterized by the usage of a restricted repetoire of variable region gene segments. +comment: Note that NK T cells are a distinct lineage of T cells expressing natural killer cell markers and having T cell receptors characterized by the usage of a restricted repertoire of variable region gene segments. synonym: "natural killer T cell activation" EXACT [] synonym: "natural T cell activation" EXACT [] synonym: "NK T lymphocyte activation" EXACT [] @@ -94582,7 +94717,7 @@ relationship: has_primary_input GO:0031982 ! vesicle id: GO:0051649 name: establishment of localization in cell namespace: biological_process -def: "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] +def: "Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] synonym: "establishment of intracellular localization" NARROW [] synonym: "establishment of localisation in cell" EXACT [GOC:mah] @@ -95535,7 +95670,6 @@ name: imidazole-containing compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." [GOC:curators] synonym: "imidazole metabolism" EXACT [] -is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24780 @@ -96191,7 +96325,7 @@ relationship: results_in_acquisition_of_features_of CL:0007005 ! notochordal cel id: GO:0060037 name: pharyngeal system development namespace: biological_process -def: "The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear." [GOC:dph] +def: "The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the structure it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear." [GOC:dph] is_a: GO:0048731 ! system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0008814 ! pharyngeal arch system @@ -96363,7 +96497,7 @@ relationship: results_in_development_of UBERON:0000995 ! uterus id: GO:0060066 name: oviduct development namespace: biological_process -def: "The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." [GOC:dph, GOC:ebc, http://www.thefreedictionary.com/oviduct] +def: "The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." [GOC:dph, GOC:ebc, PMID:22918811, PMID:27875265] synonym: "fallopian tube development" NARROW [GOC:bf] synonym: "Mullerian tract development" RELATED [] is_a: GO:0035295 ! tube development @@ -97132,7 +97266,7 @@ id: GO:0060271 name: cilium assembly namespace: biological_process alt_id: GO:0042384 -def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2] +def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441] comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. synonym: "ciliogenesis" EXACT [] synonym: "cilium biogenesis" RELATED [GOC:mah] @@ -97140,7 +97274,6 @@ synonym: "cilium formation" EXACT [] synonym: "cilium morphogenesis" RELATED [] synonym: "cilium organization" RELATED [GOC:dph] synonym: "microtubule-based flagellum assembly" EXACT [] -xref: Reactome:R-HSA-5617833.2 is_a: GO:0044782 ! cilium organization is_a: GO:0070925 ! organelle assembly is_a: GO:0120031 ! plasma membrane bounded cell projection assembly @@ -98369,8 +98502,8 @@ synonym: "small alveolar cell differentiation" RELATED [GOC:dph, ISBN:0721662544 synonym: "squamous alveolar cell differentiation" RELATED [GOC:dph, ISBN:0721662544] is_a: GO:0060487 ! lung epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:0002062 ! type I pneumocyte -relationship: results_in_acquisition_of_features_of CL:0002062 ! type I pneumocyte +intersection_of: results_in_acquisition_of_features_of CL:0002062 ! pulmonary alveolar type 1 cell +relationship: results_in_acquisition_of_features_of CL:0002062 ! pulmonary alveolar type 1 cell [Term] id: GO:0060510 @@ -98382,8 +98515,8 @@ synonym: "great alveolar cell differentiation" EXACT [GOC:dph, ISBN:0721662544] synonym: "large alveolar cell differentiation" RELATED [GOC:dph, ISBN:0721662544] is_a: GO:0061140 ! lung secretory cell differentiation intersection_of: GO:0030154 ! cell differentiation -intersection_of: results_in_acquisition_of_features_of CL:0002063 ! type II pneumocyte -relationship: results_in_acquisition_of_features_of CL:0002063 ! type II pneumocyte +intersection_of: results_in_acquisition_of_features_of CL:0002063 ! pulmonary alveolar type 2 cell +relationship: results_in_acquisition_of_features_of CL:0002063 ! pulmonary alveolar type 2 cell [Term] id: GO:0060512 @@ -103906,19 +104039,6 @@ relationship: part_of GO:0061682 ! seminal vesicle morphogenesis created_by: dph creation_date: 2015-03-04T13:39:47Z -[Term] -id: GO:0061687 -name: detoxification of inorganic compound -namespace: biological_process -def: "Any process that reduces or removes the toxicity of inorganic compounds. These include transport of such compounds away from sensitive areas and to compartments or complexes whose purpose is sequestration of inorganic compounds." [GOC:vw] -is_a: BFO:0000003 -is_a: GO:0098754 ! detoxification -intersection_of: GO:0098754 ! detoxification -intersection_of: has_primary_input CHEBI:24835 -relationship: has_primary_input CHEBI:24835 -created_by: dph -creation_date: 2015-03-09T09:16:23Z - [Term] id: GO:0061695 name: transferase complex, transferring phosphorus-containing groups @@ -106097,16 +106217,6 @@ intersection_of: has_primary_input CHEBI:24875 created_by: mah creation_date: 2009-12-10T03:57:22Z -[Term] -id: GO:0071310 -name: cellular response to organic substance -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." [GOC:mah] -is_a: GO:0010033 ! response to organic substance -is_a: GO:0070887 ! cellular response to chemical stimulus -created_by: mah -creation_date: 2009-12-10T04:46:04Z - [Term] id: GO:0071318 name: cellular response to ATP @@ -106127,7 +106237,7 @@ name: cellular response to carbohydrate stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus." [GOC:mah] is_a: GO:0009743 ! response to carbohydrate -is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:16646 created_by: mah @@ -106164,7 +106274,6 @@ name: cellular response to cytokine stimulus namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." [GOC:mah] is_a: GO:0034097 ! response to cytokine -is_a: GO:0071310 ! cellular response to organic substance created_by: mah creation_date: 2009-12-11T02:41:12Z @@ -106284,7 +106393,7 @@ name: cellular response to lipid namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus." [GOC:mah] is_a: GO:0033993 ! response to lipid -is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0070887 ! cellular response to chemical stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:18059 created_by: mah @@ -106303,19 +106412,6 @@ relationship: has_primary_input GO:1990777 ! lipoprotein particle created_by: mah creation_date: 2009-12-14T02:48:51Z -[Term] -id: GO:0071407 -name: cellular response to organic cyclic compound -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." [GOC:mah] -synonym: "cellular response to organic cyclic substance" EXACT [GOC:mah] -is_a: GO:0014070 ! response to organic cyclic compound -is_a: GO:0071310 ! cellular response to organic substance -intersection_of: GO:0070887 ! cellular response to chemical stimulus -intersection_of: has_primary_input CHEBI:33832 -created_by: mah -creation_date: 2009-12-14T02:55:58Z - [Term] id: GO:0071417 name: cellular response to organonitrogen compound @@ -106323,7 +106419,7 @@ namespace: biological_process def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [GOC:mah] synonym: "cellular response to organic nitrogen" EXACT [GOC:mah] is_a: GO:0010243 ! response to organonitrogen compound -is_a: GO:0071310 ! cellular response to organic substance +is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:0071495 ! cellular response to endogenous stimulus intersection_of: GO:0070887 ! cellular response to chemical stimulus intersection_of: has_primary_input CHEBI:35352 @@ -106721,37 +106817,6 @@ relationship: results_in_maturation_of UBERON:0003050 ! olfactory placode created_by: mah creation_date: 2010-03-02T01:10:54Z -[Term] -id: GO:0071702 -name: organic substance transport -namespace: biological_process -def: "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [GOC:mah] -is_a: BFO:0000003 -is_a: GO:0006810 ! transport -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input CHEBI:50860 -relationship: has_primary_input CHEBI:50860 -created_by: mah -creation_date: 2010-03-08T02:15:14Z - -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: BFO:0000003 -is_a: GO:0008152 ! metabolic process -intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:50860 -relationship: has_primary_input_or_output CHEBI:50860 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071705 name: nitrogen compound transport @@ -107284,7 +107349,7 @@ creation_date: 2010-10-18T03:44:18Z id: GO:0072001 name: renal system development namespace: biological_process -def: "The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels." [GOC:mtg_kidney_jan10, GOC:yaf, http://en.wikibooks.org/wiki/Human_Physiology/The_Urinary_System] +def: "The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels." [GOC:mtg_kidney_jan10, GOC:yaf, PMID:6996269] subset: gocheck_do_not_annotate synonym: "urinary system development" BROAD [GOC:yaf] synonym: "urinary tract development" BROAD [GOC:yaf, PMID:17881463] @@ -107621,6 +107686,34 @@ relationship: results_in_development_of UBERON:0004195 ! short nephron created_by: mah creation_date: 2010-01-25T02:49:32Z +[Term] +id: GO:0072031 +name: proximal convoluted tubule segment 1 development +namespace: biological_process +def: "The process whose specific outcome is the progression of the S1 portion of the proximal convoluted tubule over time, from its formation to the mature structure. The S1 portion is the initial portion of the proximal convoluted tubule and is responsible for avid reabsorption of water and solutes." [GOC:mtg_kidney_jan10, MA:0002612] +synonym: "S1 development" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0035295 ! tube development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0004196 ! proximal convoluted tubule segment 1 +relationship: part_of GO:0072019 ! proximal convoluted tubule development +relationship: results_in_development_of UBERON:0004196 ! proximal convoluted tubule segment 1 +created_by: mah +creation_date: 2010-01-25T02:55:57Z + +[Term] +id: GO:0072032 +name: proximal convoluted tubule segment 2 development +namespace: biological_process +def: "The process whose specific outcome is the progression of the S2 portion of the proximal convoluted tubule over time, from its formation to the mature structure. The S2 portion of the tubule is involved in reabsorption of water and sodium chloride." [GOC:mtg_kidney_jan10, MA:0002613] +synonym: "S2 development" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0035295 ! tube development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0004197 ! proximal convoluted tubule segment 2 +relationship: part_of GO:0072019 ! proximal convoluted tubule development +relationship: results_in_development_of UBERON:0004197 ! proximal convoluted tubule segment 2 +created_by: mah +creation_date: 2010-01-25T02:56:36Z + [Term] id: GO:0072033 name: renal vesicle formation @@ -109329,6 +109422,20 @@ relationship: results_in_development_of UBERON:0005125 ! metanephric proximal st created_by: mah creation_date: 2010-03-18T03:38:53Z +[Term] +id: GO:0072231 +name: metanephric proximal convoluted tubule segment 1 development +namespace: biological_process +def: "The process whose specific outcome is the progression of the S1 portion of the metanephric proximal convoluted tubule over time, from its formation to the mature structure. The S1 portion is the initial portion of the metanephric proximal convoluted tubule and is responsible for avid reabsorption of water and solutes." [GOC:bf, GOC:mtg_kidney_jan10] +synonym: "metanephric S1 development" EXACT [GOC:mtg_kidney_jan10] +is_a: GO:0072031 ! proximal convoluted tubule segment 1 development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0005126 ! metanephric S1 +relationship: part_of GO:0072229 ! metanephric proximal convoluted tubule development +relationship: results_in_development_of UBERON:0005126 ! metanephric S1 +created_by: mah +creation_date: 2010-03-18T03:39:10Z + [Term] id: GO:0072233 name: metanephric thick ascending limb development @@ -110270,7 +110377,7 @@ synonym: "endothelial cell programmed cell death by apoptosis" EXACT [GOC:mah] synonym: "killing of endothelial cells" EXACT [GOC:mah] synonym: "programmed cell death of endothelial cells by apoptosis" EXACT [GOC:mah] synonym: "programmed cell death, endothelial cells" EXACT [GOC:mah] -is_a: GO:1904019 ! epithelial cell apoptotic process +is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000115 ! endothelial cell relationship: occurs_in CL:0000115 ! endothelial cell @@ -111813,7 +111920,7 @@ creation_date: 2010-03-12T04:08:26Z id: GO:0090300 name: positive regulation of neural crest formation namespace: biological_process -def: "Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." [GOC:tb] +def: "Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds." [GOC:tb] is_a: GO:0010718 ! positive regulation of epithelial to mesenchymal transition is_a: GO:0090299 ! regulation of neural crest formation intersection_of: GO:0065007 ! biological regulation @@ -111826,7 +111933,7 @@ creation_date: 2010-03-12T04:08:26Z id: GO:0090301 name: negative regulation of neural crest formation namespace: biological_process -def: "Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." [GOC:tb] +def: "Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds." [GOC:tb] is_a: GO:0010719 ! negative regulation of epithelial to mesenchymal transition is_a: GO:0090299 ! regulation of neural crest formation intersection_of: GO:0065007 ! biological regulation @@ -112321,7 +112428,7 @@ creation_date: 2011-04-01T10:08:42Z id: GO:0097029 name: mature conventional dendritic cell differentiation namespace: biological_process -def: "The process in which antigen-activated dendritic cells acquire the specialized features of a mature conventional dendritic cell. Mature conventional dendritic cells upregulate the surface expression of MHC molecules, chemokine receptors and adhesion molecules, and increase the number of dendrites (cytoplasmic protrusions) in preparation for migration to lymphoid organs where they present antigen to T cells." [GOC:BHF, http://www.rndsystems.com/mini_review_detail_objectname_MR02_DendriticCellMat.aspx, PMID:15845453] +def: "The process in which antigen-activated dendritic cells acquire the specialized features of a mature conventional dendritic cell. Mature conventional dendritic cells upregulate the surface expression of MHC molecules, chemokine receptors and adhesion molecules, and increase the number of dendrites (cytoplasmic protrusions) in preparation for migration to lymphoid organs where they present antigen to T cells." [GOC:BHF, PMID:15845453] comment: Note that immunologists typically use the word 'maturation' to refer to dendritic cells undergoing the process that GO describes as 'cell differentiation'. is_a: GO:0002573 ! myeloid leukocyte differentiation is_a: GO:0097028 ! dendritic cell differentiation @@ -112513,19 +112620,6 @@ relationship: results_in_acquisition_of_features_of CL:0000617 ! GABAergic neuro created_by: pr creation_date: 2011-09-14T09:39:11Z -[Term] -id: GO:0097159 -name: organic cyclic compound binding -namespace: molecular_function -def: "Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [GOC:sjw, PMID:7583672] -is_a: BFO:0000003 -is_a: GO:0005488 ! binding -intersection_of: GO:0005488 ! binding -intersection_of: has_primary_input CHEBI:33832 -relationship: has_primary_input CHEBI:33832 -created_by: pr -creation_date: 2011-09-23T02:31:01Z - [Term] id: GO:0097164 name: ammonium ion metabolic process @@ -113164,11 +113258,10 @@ creation_date: 2016-03-29T17:39:45Z id: GO:0097711 name: ciliary basal body-plasma membrane docking namespace: biological_process -def: "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane." [GOC:cilia, PMID:13978319, PMID:23348840, PMID:23530209, PMID:25686250, PMID:26981235, Reactome:R-HSA-5620912.1] +def: "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane." [GOC:cilia, PMID:13978319, PMID:23348840, PMID:23530209, PMID:25686250, PMID:26981235] comment: Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella. synonym: "anchoring of the basal body to the plasma membrane" RELATED [] synonym: "ciliary basal body docking" EXACT [] -xref: Reactome:R-HSA-5620912.1 is_a: GO:0140056 ! organelle localization by membrane tethering relationship: part_of GO:0060271 ! cilium assembly created_by: pr @@ -113178,7 +113271,7 @@ creation_date: 2016-08-05T16:12:33Z id: GO:0097712 name: vesicle targeting, trans-Golgi to periciliary membrane compartment namespace: biological_process -def: "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces." [GOC:cilia, PMID:20106869, PMID:23351793, PMID:24814148, PMID:26485645, Reactome:R-HSA-5620920.1] +def: "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces." [GOC:cilia, PMID:20106869, PMID:23351793, PMID:24814148, PMID:26485645] is_a: GO:0048199 ! vesicle targeting, to, from or within Golgi relationship: part_of GO:0060271 ! cilium assembly created_by: pr @@ -113334,6 +113427,18 @@ intersection_of: results_in_organization_of GO:0098522 ! neuromuscular junction relationship: part_of GO:0048741 ! skeletal muscle fiber development relationship: results_in_organization_of GO:0098522 ! neuromuscular junction of skeletal muscle fiber +[Term] +id: GO:0098531 +name: ligand-activated transcription factor activity +namespace: molecular_function +def: "A DNA-binding transcription factor activity regulated by binding to a ligand and that modulates the transcription of specific genes and gene sets. Examples include the lac and trp repressors in E.coli and steroid hormone receptors." [GOC:dos, PMID:25568920, PMID:8735275] +comment: For usage guidance, see comment in GO:0003700 ; DNA-binding transcription factor activity. +synonym: "direct ligand regulated sequence-specific DNA binding transcription factor activity" EXACT [] +synonym: "transcription factor activity, direct ligand regulated sequence-specific DNA binding" EXACT [] +is_a: GO:0003700 ! DNA-binding transcription factor activity +created_by: dos +creation_date: 2013-10-17T15:51:30Z + [Term] id: GO:0098537 name: obsolete lobed nucleus @@ -113988,6 +114093,15 @@ def: "A cell projection supported by an assembly of actin filaments, and which l is_a: GO:0120025 ! plasma membrane bounded cell projection relationship: has_part GO:0005884 ! actin filament +[Term] +id: GO:0098862 +name: cluster of actin-based cell projections +namespace: cellular_component +def: "A cell part consisting of multiple, closely packed actin-based cell projections." [GOC:dos] +is_a: GO:0110165 ! cellular anatomical entity +relationship: has_part GO:0098858 ! actin-based cell projection +relationship: part_of CL:0000000 ! cell + [Term] id: GO:0098867 name: intramembranous bone growth @@ -114329,7 +114443,7 @@ relationship: occurs_in GO:0032839 ! dendrite cytoplasm id: GO:0098960 name: postsynaptic neurotransmitter receptor activity namespace: molecular_function -def: "Neurotransmitter receptor activity occuring in the postsynaptic membrane during synaptic transmission." [GOC:dos, GOC:signaling] +def: "Neurotransmitter receptor activity occurring in the postsynaptic membrane during synaptic transmission." [GOC:dos, GOC:signaling] synonym: "neurotransmitter receptor activity involved in chemical synaptic transmission" EXACT [] is_a: BFO:0000003 is_a: GO:0030594 ! neurotransmitter receptor activity @@ -114358,7 +114472,7 @@ relationship: occurs_in GO:0032839 ! dendrite cytoplasm id: GO:0098962 name: regulation of postsynaptic neurotransmitter receptor activity namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity involved in synaptic transmission. Modulation may be via an effect on ligand affinity, or effector funtion such as ion selectivity or pore opening/closing in ionotropic receptors." [GOC:dos] +def: "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity involved in synaptic transmission. Modulation may be via an effect on ligand affinity, or effector function such as ion selectivity or pore opening/closing in ionotropic receptors." [GOC:dos] subset: gocheck_do_not_annotate subset: goslim_synapse is_a: GO:0031644 ! regulation of nervous system process @@ -114604,7 +114718,7 @@ intersection_of: process_has_causal_agent CHEBI:60466 id: GO:0099083 name: retrograde trans-synaptic signaling by neuropeptide, modulating synaptic transmission namespace: biological_process -def: "Modulation of synaptic transmittion by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide." [GOC:bf, GOC:dos, GOC:PARL, PMID:19448629] +def: "Modulation of synaptic transmission by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide." [GOC:bf, GOC:dos, GOC:PARL, PMID:19448629] comment: Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua. subset: goslim_synapse is_a: GO:0099082 ! retrograde trans-synaptic signaling by neuropeptide @@ -115439,7 +115553,7 @@ relationship: has_small_molecule_activator CHEBI:350546 id: GO:0099601 name: regulation of neurotransmitter receptor activity namespace: biological_process -def: "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity. Modulation may be via an effect on ligand affinity, or effector funtion such as ion selectivity or pore opening/closing in ionotropic receptors." [GOC:dos] +def: "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity. Modulation may be via an effect on ligand affinity, or effector function such as ion selectivity or pore opening/closing in ionotropic receptors." [GOC:dos] subset: gocheck_do_not_annotate subset: goslim_synapse is_a: GO:0010469 ! regulation of signaling receptor activity @@ -115886,8 +116000,8 @@ def: "High affinity ammonium transporter complex that enables the transfer of am synonym: "AMT1 complex" NARROW [GOC:bhm] is_a: GO:1902495 ! transmembrane transporter complex intersection_of: GO:0032991 ! protein-containing complex -intersection_of: capable_of GO:0008519 ! ammonium transmembrane transporter activity -relationship: capable_of GO:0008519 ! ammonium transmembrane transporter activity +intersection_of: capable_of GO:0008519 ! ammonium channel activity +relationship: capable_of GO:0008519 ! ammonium channel activity relationship: capable_of_part_of GO:0072488 ! ammonium transmembrane transport created_by: kmv creation_date: 2017-11-20T15:21:10Z @@ -116541,6 +116655,99 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: krc creation_date: 2018-08-14T23:05:40Z +[Term] +id: GO:0120213 +name: regulation of histidine biosynthetic process +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of histidine biosynthetic process." [GOC:krc] +synonym: "regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "regulation of histidine formation" EXACT [GOC:krc] +synonym: "regulation of histidine synthesis" EXACT [GOC:krc] +is_a: GO:0009889 ! regulation of biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0000105 ! L-histidine biosynthetic process +relationship: regulates GO:0000105 ! L-histidine biosynthetic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17537" xsd:anyURI +created_by: krc +creation_date: 2019-06-27T20:55:42Z + +[Term] +id: GO:0120214 +name: negative regulation of histidine biosynthetic process +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of histidine biosynthetic process." [GOC:krc] +synonym: "down regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "down regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "down regulation of histidine biosynthetic process" EXACT [GOC:krc] +synonym: "down regulation of histidine formation" EXACT [GOC:krc] +synonym: "down regulation of histidine synthesis" EXACT [GOC:krc] +synonym: "down-regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "down-regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "down-regulation of histidine biosynthetic process" EXACT [GOC:krc] +synonym: "down-regulation of histidine formation" EXACT [GOC:krc] +synonym: "down-regulation of histidine synthesis" EXACT [GOC:krc] +synonym: "downregulation of histidine anabolism" EXACT [GOC:krc] +synonym: "downregulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "downregulation of histidine biosynthetic process" EXACT [GOC:krc] +synonym: "downregulation of histidine formation" EXACT [GOC:krc] +synonym: "downregulation of histidine synthesis" EXACT [GOC:krc] +synonym: "inhibition of histidine anabolism" NARROW [GOC:krc] +synonym: "inhibition of histidine biosynthesis" NARROW [GOC:krc] +synonym: "inhibition of histidine biosynthetic process" NARROW [GOC:krc] +synonym: "inhibition of histidine formation" NARROW [GOC:krc] +synonym: "inhibition of histidine synthesis" NARROW [GOC:krc] +synonym: "negative regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "negative regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "negative regulation of histidine formation" EXACT [GOC:krc] +synonym: "negative regulation of histidine synthesis" EXACT [GOC:krc] +is_a: GO:0009890 ! negative regulation of biosynthetic process +is_a: GO:0120213 ! regulation of histidine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0000105 ! L-histidine biosynthetic process +relationship: negatively_regulates GO:0000105 ! L-histidine biosynthetic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17537" xsd:anyURI +created_by: krc +creation_date: 2019-06-27T20:56:35Z + +[Term] +id: GO:0120215 +name: positive regulation of histidine biosynthetic process +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of histidine biosynthetic process." [GOC:krc] +synonym: "activation of histidine anabolism" NARROW [GOC:krc] +synonym: "activation of histidine biosynthesis" NARROW [GOC:krc] +synonym: "activation of histidine biosynthetic process" NARROW [GOC:krc] +synonym: "activation of histidine formation" NARROW [GOC:krc] +synonym: "activation of histidine synthesis" NARROW [GOC:krc] +synonym: "positive regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "positive regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "positive regulation of histidine formation" EXACT [GOC:krc] +synonym: "positive regulation of histidine synthesis" EXACT [GOC:krc] +synonym: "up regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "up regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "up regulation of histidine biosynthetic process" EXACT [GOC:krc] +synonym: "up regulation of histidine formation" EXACT [GOC:krc] +synonym: "up regulation of histidine synthesis" EXACT [GOC:krc] +synonym: "up-regulation of histidine anabolism" EXACT [GOC:krc] +synonym: "up-regulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "up-regulation of histidine biosynthetic process" EXACT [GOC:krc] +synonym: "up-regulation of histidine formation" EXACT [GOC:krc] +synonym: "up-regulation of histidine synthesis" EXACT [GOC:krc] +synonym: "upregulation of histidine anabolism" EXACT [GOC:krc] +synonym: "upregulation of histidine biosynthesis" EXACT [GOC:krc] +synonym: "upregulation of histidine biosynthetic process" EXACT [GOC:krc] +synonym: "upregulation of histidine formation" EXACT [GOC:krc] +synonym: "upregulation of histidine synthesis" EXACT [GOC:krc] +is_a: GO:0009891 ! positive regulation of biosynthetic process +is_a: GO:0120213 ! regulation of histidine biosynthetic process +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0000105 ! L-histidine biosynthetic process +relationship: positively_regulates GO:0000105 ! L-histidine biosynthetic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17537" xsd:anyURI +created_by: krc +creation_date: 2019-06-27T20:57:28Z + [Term] id: GO:0120222 name: regulation of blastocyst development @@ -117177,6 +117384,7 @@ is_a: GO:0030163 ! protein catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse +relationship: has_primary_input CHEBI:36080 relationship: occurs_in GO:0045202 ! synapse relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa @@ -117592,11 +117800,13 @@ namespace: biological_process def: "The biosynthetic process resulting in the formation of a nucleic acid." [GOC:dph, GOC:tb] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate +is_a: GO:0009058 ! biosynthetic process is_a: GO:0090304 ! nucleic acid metabolic process -intersection_of: GO:0008152 ! metabolic process +intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33696 relationship: has_primary_output CHEBI:33696 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27408" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27633" xsd:anyURI created_by: pg creation_date: 2024-03-25T07:33:40Z @@ -117607,20 +117817,24 @@ namespace: biological_process def: "The cellular DNA metabolic process resulting in the breakdown of a nucleic acid." [GOC:curators] comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term. subset: gocheck_do_not_annotate +is_a: GO:0009056 ! catabolic process is_a: GO:0090304 ! nucleic acid metabolic process -intersection_of: GO:0008152 ! metabolic process +intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:33696 relationship: has_primary_input CHEBI:33696 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27408" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27633" xsd:anyURI created_by: pg creation_date: 2024-03-25T07:35:06Z [Term] id: GO:0141193 -name: nuclear receptor signaling pathway +name: nuclear receptor-mediated signaling pathway namespace: biological_process -def: "The series of molecular signals initiated by a signaling molecule binding to its nuclear receptor inside the cell, and ending with the regulation of a downstream cellular process, e.g. transcription." [PMID:25614732] +def: "The series of molecular signals initiated by a signaling molecule binding to an intracellular receptor of the nuclear receptor protein family, and ending with regulation of a downstream cellular process, e.g. transcription." [PMID:25614732] +synonym: "nuclear receptor signaling pathway" EXACT [] is_a: GO:0030522 ! intracellular receptor signaling pathway +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27599" xsd:anyURI created_by: pg creation_date: 2024-04-12T13:08:13Z @@ -118057,7 +118271,7 @@ creation_date: 2023-08-29T21:05:28Z id: GO:0160133 name: bicarbonate channel activity namespace: molecular_function -def: "Enables the facilitated diffusion of a bicarbonate (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [PMID:18400985] +def: "Enables the energy-independent facilitated diffusion of bicarbonate through a transmembrane aqueous pore or channel." [PMID:18400985] synonym: "hydrogencarbonate channel activity" EXACT [] is_a: GO:0015106 ! bicarbonate transmembrane transporter activity is_a: GO:0015267 ! channel activity @@ -120586,52 +120800,6 @@ relationship: negatively_regulates GO:0001944 ! vasculature development created_by: bf creation_date: 2012-09-06T09:17:24Z -[Term] -id: GO:1901360 -name: organic cyclic compound metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] -synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie] -is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:33832 -relationship: has_primary_input_or_output CHEBI:33832 -created_by: bf -creation_date: 2012-09-14T09:03:51Z - -[Term] -id: GO:1901361 -name: organic cyclic compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." [GOC:TermGenie] -synonym: "organic cyclic compound breakdown" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound catabolism" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound degradation" EXACT [GOC:TermGenie] -is_a: GO:0009056 ! catabolic process -is_a: GO:1901360 ! organic cyclic compound metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:33832 -relationship: has_primary_input CHEBI:33832 -created_by: bf -creation_date: 2012-09-14T09:05:04Z - -[Term] -id: GO:1901362 -name: organic cyclic compound biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of organic cyclic compound." [GOC:TermGenie] -synonym: "organic cyclic compound anabolism" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound formation" EXACT [GOC:TermGenie] -synonym: "organic cyclic compound synthesis" EXACT [GOC:TermGenie] -is_a: GO:1901360 ! organic cyclic compound metabolic process -is_a: GO:1901576 ! organic substance biosynthetic process -intersection_of: GO:0009058 ! biosynthetic process -intersection_of: has_primary_output CHEBI:33832 -relationship: has_primary_output CHEBI:33832 -created_by: bf -creation_date: 2012-09-14T09:05:22Z - [Term] id: GO:1901382 name: regulation of chorionic trophoblast cell proliferation @@ -120907,7 +121075,8 @@ namespace: biological_process def: "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] subset: gocheck_do_not_annotate synonym: "organonitrogen compound metabolism" EXACT [GOC:TermGenie] -is_a: GO:0071704 ! organic substance metabolic process +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:35352 relationship: has_primary_input_or_output CHEBI:35352 @@ -120943,8 +121112,8 @@ synonym: "organonitrogen compound anabolism" EXACT [GOC:TermGenie] synonym: "organonitrogen compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organonitrogen compound formation" EXACT [GOC:TermGenie] synonym: "organonitrogen compound synthesis" EXACT [GOC:TermGenie] +is_a: GO:0009058 ! biosynthetic process is_a: GO:1901564 ! organonitrogen compound metabolic process -is_a: GO:1901576 ! organic substance biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:35352 relationship: has_primary_output CHEBI:35352 @@ -120952,49 +121121,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pr creation_date: 2012-11-04T15:18:00Z -[Term] -id: GO:1901575 -name: organic substance catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity catabolic process" EXACT [] -synonym: "organic substance breakdown" EXACT [] -synonym: "organic substance catabolism" EXACT [] -synonym: "organic substance degradation" EXACT [] -is_a: GO:0009056 ! catabolic process -is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:50860 -relationship: has_primary_input CHEBI:50860 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:36Z - -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -intersection_of: GO:0009058 ! biosynthetic process -intersection_of: has_primary_output CHEBI:50860 -relationship: has_primary_output CHEBI:50860 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1901588 name: dendritic microtubule @@ -121220,7 +121346,8 @@ name: organic hydroxy compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic hydroxy compound." [GOC:pr, GOC:TermGenie] synonym: "organic hydroxy compound metabolism" EXACT [GOC:TermGenie] -is_a: GO:0071704 ! organic substance metabolic process +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:33822 relationship: has_primary_input_or_output CHEBI:33822 @@ -121252,7 +121379,7 @@ synonym: "organic hydroxy compound anabolism" EXACT [GOC:TermGenie] synonym: "organic hydroxy compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organic hydroxy compound formation" EXACT [GOC:TermGenie] synonym: "organic hydroxy compound synthesis" EXACT [GOC:TermGenie] -is_a: GO:1901576 ! organic substance biosynthetic process +is_a: GO:0009058 ! biosynthetic process is_a: GO:1901615 ! organic hydroxy compound metabolic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:33822 @@ -121441,7 +121568,8 @@ namespace: biological_process alt_id: GO:1990369 def: "A response that results in a state of tolerance to ketone." [GOC:mengo_curators, PMID:23356676] synonym: "process resulting in tolerance to ketone" NARROW [] -is_a: GO:0010033 ! response to organic substance +is_a: BFO:0000003 +is_a: GO:0050896 ! response to stimulus intersection_of: GO:0050896 ! response to stimulus intersection_of: has_primary_input CHEBI:17087 relationship: has_primary_input CHEBI:17087 @@ -123166,7 +123294,6 @@ synonym: "negative regulation of RNA breakdown" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA catabolism" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA degradation" EXACT [GOC:TermGenie] is_a: GO:0009895 ! negative regulation of catabolic process -is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0051253 ! negative regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006401 ! RNA catabolic process @@ -124130,7 +124257,6 @@ namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of a respiratory basal cell." [GO_REF:0000086, GOC:TermGenie, MP:0011114, PMID:17909629] comment: Changes in the lineage choice of ABCs or their undifferentiated daughters might contribute to the mucous cell hyperplasia, metaplasia or squamous metaplasia seen in many respiratory disorders synonym: "airway basal cell differentiation" EXACT [MP:0011114] -is_a: GO:0030855 ! epithelial cell differentiation is_a: GO:0048863 ! stem cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002633 ! respiratory basal cell @@ -133570,6 +133696,20 @@ relationship: results_in_movement_of CL:0000189 ! slow muscle cell created_by: ymb creation_date: 2016-02-16T21:20:11Z +[Term] +id: GO:1904970 +name: brush border assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of adjacent microvilli through the formation of Ca(2+)-dependent adhesion links between them, forming a brush border." [GO_REF:0000079, GOC:lb, GOC:TermGenie, PMID:24725409] +synonym: "brush border formation" EXACT [GOC:TermGenie] +is_a: GO:0022607 ! cellular component assembly +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:0005903 ! brush border +relationship: results_in_assembly_of GO:0005903 ! brush border +property_value: RO:0002161 NCBITaxon:4751 +created_by: tb +creation_date: 2016-02-17T00:58:30Z + [Term] id: GO:1904977 name: lymphatic endothelial cell migration @@ -140025,8 +140165,8 @@ def: "Any process that modulates the frequency, rate or extent of glucocorticoid synonym: "regulation of glucocorticoid receptor signalling pathway" EXACT [GOC:obol] is_a: GO:0033143 ! regulation of intracellular steroid hormone receptor signaling pathway intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:0042921 ! intracellular glucocorticoid receptor signaling pathway -relationship: regulates GO:0042921 ! intracellular glucocorticoid receptor signaling pathway +intersection_of: regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway +relationship: regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway created_by: vk creation_date: 2011-01-18T04:38:10Z @@ -140039,8 +140179,8 @@ synonym: "negative regulation of glucocorticoid receptor signalling pathway" EXA is_a: GO:0033144 ! negative regulation of intracellular steroid hormone receptor signaling pathway is_a: GO:2000322 ! regulation of glucocorticoid receptor signaling pathway intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0042921 ! intracellular glucocorticoid receptor signaling pathway -relationship: negatively_regulates GO:0042921 ! intracellular glucocorticoid receptor signaling pathway +intersection_of: negatively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway +relationship: negatively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway created_by: vk creation_date: 2011-01-18T04:38:43Z @@ -140053,8 +140193,8 @@ synonym: "positive regulation of glucocorticoid receptor signalling pathway" EXA is_a: GO:0033145 ! positive regulation of intracellular steroid hormone receptor signaling pathway is_a: GO:2000322 ! regulation of glucocorticoid receptor signaling pathway intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0042921 ! intracellular glucocorticoid receptor signaling pathway -relationship: positively_regulates GO:0042921 ! intracellular glucocorticoid receptor signaling pathway +intersection_of: positively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway +relationship: positively_regulates GO:0042921 ! nuclear receptor-mediated glucocorticoid signaling pathway created_by: vk creation_date: 2011-01-18T04:39:05Z @@ -140086,7 +140226,7 @@ synonym: "regulation of endothelial cell programmed cell death by apoptosis" EXA synonym: "regulation of killing of endothelial cells" EXACT [GOC:obol] synonym: "regulation of programmed cell death of endothelial cells by apoptosis" EXACT [GOC:obol] synonym: "regulation of programmed cell death, endothelial cells" EXACT [GOC:obol] -is_a: GO:1904035 ! regulation of epithelial cell apoptotic process +is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0072577 ! endothelial cell apoptotic process relationship: regulates GO:0072577 ! endothelial cell apoptotic process @@ -140104,7 +140244,7 @@ synonym: "negative regulation of endothelial cell programmed cell death by apopt synonym: "negative regulation of killing of endothelial cells" EXACT [GOC:obol] synonym: "negative regulation of programmed cell death of endothelial cells by apoptosis" EXACT [GOC:obol] synonym: "negative regulation of programmed cell death, endothelial cells" EXACT [GOC:obol] -is_a: GO:1904036 ! negative regulation of epithelial cell apoptotic process +is_a: GO:0043066 ! negative regulation of apoptotic process is_a: GO:2000351 ! regulation of endothelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0072577 ! endothelial cell apoptotic process @@ -140123,7 +140263,7 @@ synonym: "positive regulation of endothelial cell programmed cell death by apopt synonym: "positive regulation of killing of endothelial cells" EXACT [GOC:obol] synonym: "positive regulation of programmed cell death of endothelial cells by apoptosis" EXACT [GOC:obol] synonym: "positive regulation of programmed cell death, endothelial cells" EXACT [GOC:obol] -is_a: GO:1904037 ! positive regulation of epithelial cell apoptotic process +is_a: GO:0043065 ! positive regulation of apoptotic process is_a: GO:2000351 ! regulation of endothelial cell apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0072577 ! endothelial cell apoptotic process @@ -142207,6 +142347,21 @@ relationship: negatively_regulates GO:0051450 ! myoblast proliferation created_by: pr creation_date: 2011-07-12T03:06:04Z +[Term] +id: GO:2000825 +name: positive regulation of androgen receptor activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of androgen receptor activity." [GOC:obol] +subset: gocheck_do_not_annotate +is_a: GO:0006357 ! regulation of transcription by RNA polymerase II +is_a: GO:0051091 ! positive regulation of DNA-binding transcription factor activity +is_a: GO:2000273 ! positive regulation of signaling receptor activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0004879 ! nuclear receptor activity +relationship: positively_regulates GO:0004879 ! nuclear receptor activity +created_by: yaf +creation_date: 2011-07-15T10:56:14Z + [Term] id: GO:2000826 name: regulation of heart morphogenesis @@ -145930,9 +146085,21 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z +[Term] +id: PATO:0002064 +name: fenestrated +namespace: quality +def: "A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes." [PATOC:me] +subset: cell_quality +subset: mpath_slim +subset: value_slim +is_a: PATO:0000141 ! structure +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X +creation_date: 2009-07-01T01:46:53Z + [Term] id: PATO:0002078 name: hollow @@ -145940,7 +146107,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -145952,7 +146119,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -145964,7 +146131,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0002011 ! neoplastic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:50:22Z [Term] @@ -145975,7 +146142,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -145985,7 +146152,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -145995,7 +146162,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -146007,7 +146174,7 @@ comment: Becoming flat but not necessarily completely flat. subset: value_slim synonym: "compressed" RELATED [] is_a: PATO:0001591 ! curvature -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-08-16T03:59:34Z [Term] @@ -146019,7 +146186,7 @@ subset: value_slim synonym: "channeled" RELATED [] synonym: "creased" RELATED [] is_a: PATO:0000150 ! texture -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-09-01T10:27:48Z [Term] @@ -146028,7 +146195,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -146041,7 +146208,7 @@ is_a: PATO:0001171 ! elastic is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0001171 ! elastic intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-03-30T11:50:21Z [Term] @@ -146054,7 +146221,7 @@ is_a: PATO:0001171 ! elastic is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0001171 ! elastic intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-03-30T11:50:39Z [Term] @@ -146067,7 +146234,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -146079,7 +146246,7 @@ is_a: PATO:0000069 ! deviation (from_normal) intersection_of: PATO:0000001 ! quality intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal relationship: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:39:43Z [Term] @@ -146091,7 +146258,7 @@ is_a: PATO:0000069 ! deviation (from_normal) intersection_of: PATO:0000001 ! quality intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal relationship: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:40:15Z [Term] @@ -146103,7 +146270,7 @@ is_a: PATO:0001241 ! physical object quality is_a: PATO:0002301 ! decreased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:51:54Z [Term] @@ -146115,7 +146282,7 @@ is_a: PATO:0001241 ! physical object quality is_a: PATO:0002300 ! increased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:54:01Z [Term] @@ -146126,7 +146293,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -146136,7 +146303,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -146149,7 +146316,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -146160,7 +146327,7 @@ def: "Having both hydrophilic and hydrophobic (or lipophilic) groups." [wikipedi subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:04:39Z [Term] @@ -146172,7 +146339,7 @@ comment: Acinus is Latin for berry. subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:11:10Z [Term] @@ -146182,7 +146349,7 @@ namespace: quality def: "A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material." [PATOC:WC] subset: value_slim is_a: PATO:0000025 ! composition -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-01-29T11:03:49Z [Term] @@ -146192,7 +146359,7 @@ namespace: quality def: "A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen." [PATOC:WD] subset: value_slim is_a: PATO:0000025 ! composition -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:34:15Z [Term] @@ -146202,7 +146369,7 @@ namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." [PATOC:WD] subset: value_slim is_a: PATO:0015008 ! distensibility -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:48:26Z [Term] @@ -146214,7 +146381,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:15Z [Term] @@ -146226,7 +146393,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:42Z [Term] @@ -146237,7 +146404,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -146247,7 +146414,7 @@ namespace: quality def: "A surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes." [PATOC:DOS] subset: value_slim is_a: PATO:0001925 ! surface feature shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-25T04:42:40Z [Term] @@ -146257,7 +146424,7 @@ namespace: quality def: "A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin." [PATOC:EJS] subset: value_slim is_a: PATO:0000025 ! composition -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9611-1279 +property_value: terms:contributor https://orcid.org/0000-0002-9611-1279 creation_date: 2014-02-04T12:38:14Z [Term] @@ -146266,7 +146433,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -146276,7 +146443,7 @@ namespace: quality def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z [Term] @@ -146315,7 +146482,7 @@ is_a: PATO:0001241 ! physical object quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal relationship: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-21T14:11:01Z [Term] @@ -146329,7 +146496,7 @@ is_a: PATO:0000404 ! coiled is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000404 ! coiled intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146343,7 +146510,7 @@ is_a: PATO:0001690 ! contractile is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0001690 ! contractile intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146356,7 +146523,7 @@ is_a: PATO:0001171 ! elastic is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0001171 ! elastic intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146370,7 +146537,7 @@ is_a: PATO:0001544 ! flexible is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0001544 ! flexible intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146382,7 +146549,7 @@ is_a: PATO:0000050 ! life span is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000050 ! life span intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146395,7 +146562,7 @@ is_a: PATO:0000117 ! size is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000117 ! size intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146408,7 +146575,7 @@ is_a: PATO:0000998 ! viscous is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000998 ! viscous intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 +property_value: terms:contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -146418,7 +146585,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts." [PMID:17122314] xref: ilxtr:NeurogliaformPhenotype is_a: PATO:0070026 ! multipolar neuron morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070002 @@ -146429,7 +146596,7 @@ xref: ILX:0101123 xref: ilxtr:BasketPhenotype xref: nifext:3 is_a: PATO:0070026 ! multipolar neuron morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070003 @@ -146438,7 +146605,7 @@ namespace: quality def: "A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer." [PMID:11884355] xref: ilxtr:SmallBasketPhenotype is_a: PATO:0070002 ! basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070004 @@ -146447,7 +146614,7 @@ namespace: quality def: "A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers." [PMID:11884355] xref: ilxtr:LargeBasketPhenotype is_a: PATO:0070002 ! basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070005 @@ -146456,7 +146623,7 @@ namespace: quality def: "A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches." [PMID:11884355] xref: ilxtr:NestBasketPhenotype is_a: PATO:0070002 ! basket cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070006 @@ -146468,7 +146635,7 @@ xref: ILX:0101312 xref: ilxtr:BipolarPhenotype xref: nifext:2 is_a: PATO:0070027 ! bitufted dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070007 @@ -146477,7 +146644,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching." [doi:10.1016/b978-0-12-369497-3.10004-4] xref: ilxtr:MartinottiPhenotype is_a: PATO:0070026 ! multipolar neuron morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070008 @@ -146486,7 +146653,7 @@ namespace: quality def: "A Martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped." [doi:10.1016/b978-0-12-369497-3.10004-4] synonym: "'T-shaped' Martinotti morphology" EXACT [] is_a: PATO:0070007 ! Martinotti morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070009 @@ -146495,7 +146662,7 @@ namespace: quality def: "A Martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus." [doi:10.1016/b978-0-12-369497-3.10004-4] synonym: "'fanning-out' Martinotti morphology" EXACT [] is_a: PATO:0070007 ! Martinotti morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070010 @@ -146505,7 +146672,7 @@ def: "A cell morphology that inheres in neurons that have dendritic processes ra xref: ILX:0111036 xref: SAO:9271919883 is_a: PATO:0070026 ! multipolar neuron morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070011 @@ -146517,7 +146684,7 @@ xref: ILX:0102028 xref: ilxtr:ChandelierPhenotype xref: nifext:4 is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070012 @@ -146526,7 +146693,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers." [doi:10.1016/b978-0-12-369497-3.10004-4, PMID:15378039, PMID:18568015] xref: ilxtr:BituftedPhenotype is_a: PATO:0070027 ! bitufted dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070013 @@ -146535,7 +146702,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals." [doi:10.1016/b978-0-12-369497-3.10004-4] xref: ilxtr:SpinyStellatePhenotype is_a: PATO:0070026 ! multipolar neuron morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070015 @@ -146545,7 +146712,7 @@ def: "A cell morphology that inheres in neurons which have a pyramidal shaped so xref: ILX:0109553 xref: SAO:1465673360 is_a: PATO:0070026 ! multipolar neuron morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070016 @@ -146555,7 +146722,7 @@ def: "A pyramidal family morphology that inheres in neurons which have an apical xref: ilxtr:HorizontalPyramidalPhenotype is_a: PATO:0070015 ! pyramidal family morphology disjoint_from: PATO:0070017 ! standard pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070017 @@ -146566,7 +146733,7 @@ synonym: "pyramidal cell morphology" EXACT [] synonym: "vertical pyramidal morphology" EXACT [] xref: ilxtr:PyramidalPhenotype is_a: PATO:0070015 ! pyramidal family morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070018 @@ -146575,7 +146742,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma." [PMID:30715238] xref: ilxtr:TuftedPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070019 @@ -146584,7 +146751,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances." [PMID:30715238] xref: ilxtr:UntuftedPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070020 @@ -146593,7 +146760,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape." [PMID:30715238] xref: ilxtr:StarPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070021 @@ -146602,7 +146769,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter." [PMID:30715238] xref: ilxtr:InvertedPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070025 @@ -146610,7 +146777,7 @@ name: unipolar neuron morphology namespace: quality def: "A cell morphology that inheres in neurons with only one process, a neurite, that extends from the cell body. The neurite then branches to form dendritic and axonal processes." [WikipediaVersioned:Unipolar_neuron&oldid=994458581] is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070026 @@ -146620,7 +146787,7 @@ def: "A cell morphology that inheres in neurons which possess three or more neur xref: ILX:0107196 xref: NLX:378 is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070027 @@ -146629,7 +146796,7 @@ namespace: quality def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070028 @@ -146639,7 +146806,7 @@ def: "A neuron projection quality that is a characteristic of neurons whose soma synonym: "ET projecting" EXACT [] xref: ILX:0770101 is_a: PATO:0070033 ! neuron projection quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070029 @@ -146649,7 +146816,7 @@ def: "A neuron projection quality that is a characteristic of neurons with soma synonym: "CT projecting" EXACT [] xref: ILX:0770102 is_a: PATO:0070033 ! neuron projection quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070030 @@ -146659,7 +146826,7 @@ def: "A neuron projection quality that is a characteristic of neurons with proje synonym: "NP" EXACT [] xref: ILX:0770103 is_a: PATO:0070033 ! neuron projection quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070031 @@ -146668,7 +146835,7 @@ namespace: quality def: "A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions." [DOI:10.1101/2020.10.19.343129] synonym: "MY projecting" EXACT [] is_a: PATO:0070033 ! neuron projection quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070033 @@ -146676,7 +146843,7 @@ name: neuron projection quality namespace: quality def: "A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in." [DOI:10.1101/2020.10.19.343129] is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070034 @@ -146686,7 +146853,7 @@ def: "A neuron projection quality that is a characteristic of neurons with both synonym: "IT projecting" EXACT [] xref: ILX:0770100 is_a: PATO:0070033 ! neuron projection quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -146741,7 +146908,7 @@ name: bistratified dendrite cell morphology namespace: quality def: "A cell morphology that inheres in neurons with dendrites that stratify at two and only two locations." [PMID:34093409] is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070063 @@ -146749,7 +146916,7 @@ name: monostratified dendrite cell morphology namespace: quality def: "A cell morphology that inheres in neurons with dendrites that stratify at one and only one location." [PMID:34093409] is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 @@ -146759,7 +146926,10 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] -is_a: CHEBI:36080 +is_a: BFO:0000002 +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -159603,7 +159773,7 @@ intersection_of: RO:0002150 UBERON:0000996 ! continuous with vagina relationship: part_of UBERON:0000995 ! uterus relationship: RO:0002150 UBERON:0000996 ! continuous with vagina relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -159677,7 +159847,7 @@ relationship: RO:0002202 UBERON:0003050 {source="ZFA"} ! develops from olfactory relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system relationship: RO:0002433 UBERON:0001456 ! contributes to morphology of face relationship: RO:0002551 UBERON:0006813 ! has skeleton nasal skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI [Term] id: UBERON:0000005 @@ -159686,7 +159856,7 @@ namespace: uberon subset: functional_classification subset: uberon_slim synonym: "chemosensory sensory organ" EXACT [FBbt:00005157] -xref: FBbt:00005157 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005157 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000020 ! sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: capable_of GO:0007606 ! sensory perception of chemical stimulus @@ -159733,7 +159903,7 @@ relationship: has_part CL:0000696 {gci_filler="NCBITaxon:117570", gci_relation=" relationship: has_part CL:0002067 {source="PMID:16417468"} ! type A enteroendocrine cell relationship: part_of UBERON:0000016 ! endocrine pancreas relationship: RO:0002433 UBERON:0000016 ! contributes to morphology of endocrine pancreas -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -159796,7 +159966,7 @@ relationship: has_part UBERON:0002198 ! neurohypophysis relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon relationship: RO:0002495 UBERON:0034875 {source="https://orcid.org/0000-0003-3308-6245"} ! immediate transformation of future pituitary gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI [Term] id: UBERON:0000009 @@ -159823,8 +159993,8 @@ is_a: UBERON:0004923 ! organ component layer relationship: BSPO:0001107 UBERON:0000344 ! mucosa relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000010 @@ -159851,7 +160021,7 @@ xref: EHDAA2:0001445 xref: EHDAA:2893 xref: EMAPA:16665 xref: EV:0100335 -xref: FBbt:00005098 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005098 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9903 xref: GAID:715 xref: MA:0000218 @@ -159870,7 +160040,7 @@ xref: XAO:0000178 xref: ZFA:0000142 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -159913,7 +160083,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="WP", source="ZFA-modified-from-isa"} ! autonomic nervous system relationship: RO:0002433 UBERON:0002410 ! contributes to morphology of autonomic nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI [Term] id: UBERON:0000012 @@ -159974,7 +160144,7 @@ xref: ZFA:0001576 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="ZFA-modified-from-isa"} ! autonomic nervous system relationship: RO:0002433 UBERON:0002410 ! contributes to morphology of autonomic nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI [Term] id: UBERON:0000014 @@ -160003,8 +160173,8 @@ is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: has_part UBERON:0001003 ! skin epidermis relationship: has_part UBERON:0002067 ! dermis relationship: part_of UBERON:0002097 ! skin of body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg" xsd:anyURI [Term] id: UBERON:0000015 @@ -160119,7 +160289,7 @@ synonym: "insect eye" RELATED [] synonym: "Komplexauge" RELATED [BTO:0001921] synonym: "zusammengesetztes Auge" RELATED [BTO:0001921] xref: BTO:0001921 -xref: FBbt:00004508 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004508 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000217 xref: TGMA:0000024 xref: Wikipedia:Compound_eye @@ -160195,7 +160365,7 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -160210,7 +160380,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000021 @@ -160262,7 +160432,7 @@ xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 -xref: FBbt:00007000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 @@ -160320,7 +160490,7 @@ relationship: RO:0002150 UBERON:0001473 ! continuous with lymphatic vessel relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002202 UBERON:0034953 ! develops from embryonic lymph sac relationship: RO:0002473 UBERON:0001744 ! composed primarily of lymphoid tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/650" xsd:anyURI @@ -160343,7 +160513,7 @@ is_a: UBERON:0004923 ! organ component layer relationship: BSPO:0001107 UBERON:0000483 ! epithelium relationship: part_of UBERON:0000344 ! mucosa relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg" xsd:anyURI [Term] id: UBERON:0000031 @@ -160504,7 +160674,7 @@ intersection_of: has_part UBERON:0000039 ! follicular antrum relationship: has_component UBERON:0005170 ! granulosa cell layer relationship: has_part UBERON:0000039 ! follicular antrum relationship: RO:0002202 UBERON:0000036 ! develops from secondary ovarian follicle -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI [Term] id: UBERON:0000038 @@ -160537,7 +160707,7 @@ relationship: has_part UBERON:0007779 ! transudate relationship: part_of UBERON:0001305 ! ovarian follicle relationship: RO:0001025 UBERON:0000039 ! located in follicular antrum relationship: RO:0002221 CL:0000025 ! surrounds egg cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -160586,8 +160756,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000043 @@ -160623,7 +160793,7 @@ relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002176 UBERON:0001474 ! connects bone element relationship: RO:0002176 UBERON:0001630 ! connects muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI [Term] id: UBERON:0000044 @@ -160680,7 +160850,7 @@ intersection_of: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord relationship: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord relationship: RO:0002202 UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! develops from trunk neural crest -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2644" xsd:string @@ -160781,9 +160951,9 @@ is_a: UBERON:0007702 ! tract of brain relationship: extends_fibers_into UBERON:0002206 ! mammillary body relationship: extends_fibers_into UBERON:0002663 ! septal nuclear complex relationship: part_of UBERON:0002421 {source="NIFSTD"} ! hippocampal formation -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -160815,7 +160985,7 @@ is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0000054 ! macula relationship: part_of UBERON:0000966 ! retina -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI [Term] id: UBERON:0000054 @@ -160894,7 +161064,7 @@ relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0036295 ! renal pelvis/ureter relationship: RO:0002202 UBERON:0005081 {source="GO"} ! develops from ureter ureteric bud -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -160935,7 +161105,7 @@ relationship: part_of UBERON:0001556 ! lower urinary tract relationship: RO:0002150 UBERON:0001255 ! continuous with urinary bladder relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus relationship: RO:0002202 UBERON:0013241 {source="Wikipedia"} ! develops from embryonic urethral groove -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0000058 @@ -160948,7 +161118,7 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -160998,9 +161168,9 @@ relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0004907 ! lower digestive tract relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -161034,7 +161204,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -161296,7 +161466,7 @@ is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -161336,10 +161506,10 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle relationship: RO:0002202 UBERON:0005749 ! develops from glomerular tuft relationship: RO:0002219 UBERON:0001230 ! surrounded by glomerular capsule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:26:37Z [Term] @@ -161384,7 +161554,7 @@ xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string [Term] @@ -161438,7 +161608,7 @@ xref: EHDAA2:0001054 xref: EHDAA:8136 xref: EMAPA:17968 xref: EV:0100101 -xref: FBbt:00004927 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004927 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45664 xref: GAID:386 xref: HAO:0000505 @@ -161457,7 +161627,7 @@ intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003101 ! male organism disjoint_from: UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003101 ! male organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -161500,7 +161670,7 @@ xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure relationship: RO:0002202 UBERON:0002120 ! develops from pronephros -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI [Term] id: UBERON:0000081 @@ -161607,7 +161777,7 @@ relationship: part_of UBERON:0004716 {source="EHDAA2"} ! conceptus relationship: RO:0002219 UBERON:0000086 ! surrounded by zona pellucida relationship: RO:0002488 UBERON:0000107 ! existence starts during cleavage stage relationship: RO:0002492 UBERON:0000107 ! existence ends during cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI [Term] id: UBERON:0000086 @@ -161643,7 +161813,7 @@ is_a: UBERON:0005764 ! acellular membrane relationship: bounding_layer_of CL:0000023 ! oocyte relationship: has_part CHEBI:17089 relationship: part_of UBERON:0000992 ! ovary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -161673,7 +161843,7 @@ is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: RO:0002202 UBERON:0000358 {source="Wikipedia"} ! develops from blastocyst relationship: RO:0002219 UBERON:0000088 {source="Wikipedia"} ! surrounded by trophoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI [Term] id: UBERON:0000088 @@ -161702,7 +161872,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000358 ! blastocyst relationship: RO:0002202 UBERON:0004345 {source="MP-def", source="PMID:19829370"} ! develops from trophectoderm relationship: RO:0002473 CL:0000351 ! composed primarily of trophoblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI [Term] id: UBERON:0000091 @@ -161725,7 +161895,7 @@ xref: Wikipedia:Bilaminar_disc is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: RO:0002202 UBERON:0000087 {source="Wikipedia"} ! develops from inner cell mass -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI [Term] id: UBERON:0000092 @@ -161757,7 +161927,7 @@ subset: grouping_class subset: non_informative xref: Wikipedia:Sulcus_(anatomy) is_a: UBERON:0000464 ! anatomical space -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-09T06:23:22Z [Term] @@ -161770,7 +161940,7 @@ synonym: "membrane of organ" EXACT [] xref: FMA:7145 is_a: UBERON:0000062 ! organ relationship: RO:0002473 UBERON:0011823 {source="FMA-def"} ! composed primarily of dense connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-07-30T05:19:13Z [Term] @@ -161789,7 +161959,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: overlaps UBERON:0005428 {source="Wikipedia"} ! vagal neural crest relationship: part_of UBERON:0002342 ! neural crest -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-07-30T07:57:38Z [Term] @@ -161965,7 +162135,7 @@ is_a: BFO:0000003 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -162173,7 +162343,7 @@ is_a: UBERON:0005911 ! endo-epithelium relationship: adjacent_to UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0005597 ! develops from lung primordium relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png" xsd:anyURI property_value: IAO:0000116 "clarify successors - include bronchi?" xsd:string [Term] @@ -162225,7 +162395,7 @@ relationship: bounding_layer_of UBERON:0001019 ! nerve fasciculus relationship: has_part GO:0005581 ! collagen trimer relationship: part_of UBERON:0003209 ! blood nerve barrier relationship: RO:0001025 UBERON:0000124 ! located in epineurium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI [Term] id: UBERON:0000122 @@ -162237,7 +162407,7 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005099 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NLX:147821 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection @@ -162259,7 +162429,7 @@ xref: Wikipedia:Epineurium is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: part_of UBERON:0000010 ! peripheral nervous system relationship: RO:0002221 UBERON:0001021 ! surrounds nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI [Term] id: UBERON:0000125 @@ -162299,7 +162469,7 @@ is_a: UBERON:0002308 ! nucleus of brain intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: extends_fibers_into UBERON:0001785 ! cranial nerve relationship: extends_fibers_into UBERON:0001785 ! cranial nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI [Term] id: UBERON:0000127 @@ -162437,7 +162607,7 @@ relationship: part_of UBERON:0001353 ! anal region relationship: RO:0002150 UBERON:0001052 ! continuous with rectum relationship: RO:0002150 UBERON:0001245 ! continuous with anus relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI property_value: IAO:0000116 "requires alignment with EHDAA2 and complete developmental relationships" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -162561,7 +162731,7 @@ relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0000165 @@ -162595,7 +162765,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -162623,7 +162793,7 @@ intersection_of: BSPO:0001106 UBERON:0001555 ! digestive tract relationship: BSPO:0001106 UBERON:0001555 ! digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -162850,7 +163020,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -162893,7 +163063,7 @@ is_a: UBERON:0000120 ! blood brain barrier is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0000120 ! blood brain barrier intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-10T08:15:44Z [Term] @@ -162901,13 +163071,13 @@ id: UBERON:0000202 name: glial blood brain barrier namespace: uberon def: "A blood brain barrier composed of glial cells." [https://orcid.org/0000-0002-6601-2165] -xref: FBbt:00007091 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 is_a: UBERON:0000120 ! blood brain barrier intersection_of: UBERON:0000120 ! blood brain barrier intersection_of: RO:0002473 CL:0000125 ! composed primarily of glial cell relationship: RO:0002473 CL:0000125 ! composed primarily of glial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-10T08:42:24Z [Term] @@ -162934,9 +163104,9 @@ xref: Wikipedia:Pallium_(neuroanatomy) xref: ZFA:0000505 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001893 ! telencephalon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} property_value: seeAlso "https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87" xsd:anyURI +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-18T12:03:09Z [Term] @@ -162958,7 +163128,7 @@ xref: ZFA:0000304 is_a: UBERON:0002616 ! regional part of brain relationship: BSPO:0000098 UBERON:0000203 ! pallium relationship: part_of UBERON:0001893 ! telencephalon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-18T12:12:27Z [Term] @@ -162991,8 +163161,8 @@ relationship: overlaps UBERON:0001697 ! orbit of skull relationship: part_of UBERON:0003113 {source="cjm"} ! dermatocranium relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -163024,7 +163194,7 @@ xref: ZFA:0001675 is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0002384 ! connective tissue relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI [Term] id: UBERON:0000218 @@ -163079,7 +163249,7 @@ relationship: BSPO:0000126 UBERON:0006072 {source="FMA-abduced-lr"} ! cervical r relationship: part_of UBERON:0011138 ! postcranial axial skeletal system relationship: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 relationship: RO:0002176 UBERON:0001676 ! connects occipital bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI [Term] id: UBERON:0000304 @@ -163135,8 +163305,8 @@ relationship: RO:0002202 UBERON:0005971 {source="ISBN:0073040584"} ! develops fr relationship: RO:0002221 UBERON:0000922 ! surrounds embryo relationship: RO:0002254 UBERON:0000924 {source="ISBN:0073040584-table5.4"} ! has developmental contribution from ectoderm relationship: RO:0002254 UBERON:0004871 {source="ISBN:0073040584-table5.4"} ! has developmental contribution from somatic layer of lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -163160,7 +163330,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -163201,7 +163371,7 @@ xref: UMLS:C0006141 {source="ncithesaurus:Breast"} xref: Wikipedia:Breast is_a: UBERON:0034929 ! external soft tissue zone relationship: part_of UBERON:0001443 ! chest -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg" xsd:anyURI [Term] id: UBERON:0000313 @@ -163286,8 +163456,8 @@ relationship: adjacent_to UBERON:0002362 ! arachnoid mater relationship: part_of UBERON:0010743 ! meningeal cluster relationship: RO:0001015 UBERON:0001359 ! location of cerebrospinal fluid relationship: RO:0001015 UBERON:0001981 {source="ISBN:0471888893"} ! location of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png" xsd:anyURI [Term] id: UBERON:0000316 @@ -163371,7 +163541,7 @@ synonym: "fetus" NARROW [BTO:0000449] xref: BTO:0000449 xref: CALOHA:TS-0360 xref: EFO:0001323 -xref: FBbt:00005333 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005333 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63919 xref: GAID:552 xref: MESH:D005333 @@ -163558,8 +163728,8 @@ is_a: UBERON:0004923 ! organ component layer relationship: has_part UBERON:0000483 ! epithelium relationship: has_part UBERON:0002384 ! connective tissue relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000348 @@ -163638,7 +163808,7 @@ xref: Wikipedia:Limbic_system is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0001890 ! forebrain -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg" xsd:anyURI property_value: IAO:0000116 "obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity." xsd:string [Term] @@ -163747,7 +163917,7 @@ relationship: part_of UBERON:0000307 ! blastula relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria relationship: RO:0002202 UBERON:0000085 ! develops from morula relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI property_value: IAO:0000116 "Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)" xsd:string [Term] @@ -163805,11 +163975,11 @@ relationship: capable_of_part_of GO:0070295 ! renal water absorption relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -163839,7 +164009,7 @@ xref: Wikipedia:Urothelium is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0001008 ! renal system -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Harnblase_Urothel.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Harnblase_Urothel.png" xsd:anyURI [Term] id: UBERON:0000369 @@ -163869,7 +164039,7 @@ xref: VHOG:0001175 xref: Wikipedia:Corpus_striatum is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002420 {source="MA"} ! basal ganglion -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray656.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray656.png" xsd:anyURI [Term] id: UBERON:0000371 @@ -163893,7 +164063,7 @@ xref: Wikipedia:Syncytiotrophoblast is_a: UBERON:0002050 {source="FMA"} ! embryonic structure relationship: part_of UBERON:0004364 {source="EMAPA"} ! ectoplacental cone relationship: RO:0002473 CL:0000525 ! composed primarily of syncytiotrophoblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png" xsd:anyURI [Term] id: UBERON:0000375 @@ -163935,7 +164105,7 @@ xref: VHOG:0001345 xref: Wikipedia:Mandibular_nerve is_a: UBERON:0011779 ! nerve of head region relationship: RO:0002380 UBERON:0001645 ! branching part of trigeminal nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -163982,7 +164152,7 @@ intersection_of: part_of UBERON:0002103 ! hindlimb relationship: part_of UBERON:0000978 {source="MA"} ! leg relationship: RO:0002433 UBERON:0002103 ! contributes to morphology of hindlimb relationship: RO:0002551 UBERON:0015052 ! has skeleton femur endochondral element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png" xsd:anyURI [Term] id: UBERON:0000377 @@ -164020,7 +164190,7 @@ xref: VHOG:0001346 xref: Wikipedia:Maxillary_nerve is_a: UBERON:0011779 ! nerve of head region relationship: RO:0002380 UBERON:0001645 ! branching part of trigeminal nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -164058,7 +164228,7 @@ relationship: part_of UBERON:0000165 ! mouth relationship: RO:0002177 UBERON:0001723 ! attached to part of tongue relationship: RO:0002202 UBERON:0005594 {source="FEED:rd", source="ISBN:1607950324"} ! develops from head somite relationship: RO:0002433 UBERON:0001723 ! contributes to morphology of tongue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png" xsd:anyURI [Term] id: UBERON:0000379 @@ -164254,7 +164424,7 @@ relationship: extends_fibers_into UBERON:0004727 ! cochlear nerve relationship: part_of UBERON:0002827 ! vestibulocochlear ganglion relationship: part_of UBERON:0016490 ! auditory system relationship: RO:0001025 UBERON:0006723 ! located in cochlear modiolus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png" xsd:anyURI property_value: IAO:0000116 "in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems" xsd:string [Term] @@ -164362,7 +164532,7 @@ xref: SCTID:278940000 xref: Wikipedia:Nasal_vestibule is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001707 ! nasal cavity -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png" xsd:anyURI [Term] id: UBERON:0000403 @@ -164390,8 +164560,8 @@ relationship: has_part UBERON:0002515 ! periosteum relationship: overlaps UBERON:0001084 ! skin of head relationship: overlaps UBERON:0006661 ! epicranial aponeurosis relationship: part_of UBERON:0000033 {source="BTO"} ! head -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/eb/Double_cowlick.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/eb/Double_cowlick.jpg" xsd:anyURI [Term] id: UBERON:0000407 @@ -164415,7 +164585,7 @@ is_a: UBERON:0000062 ! organ is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000013 {source="FMA-abduced-lr"} ! sympathetic nervous system relationship: part_of UBERON:0000013 ! sympathetic nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI [Term] id: UBERON:0000409 @@ -164434,7 +164604,7 @@ intersection_of: has_part CL:0000313 ! serous secreting cell relationship: has_part CL:0000313 ! serous secreting cell relationship: has_part UBERON:0013232 ! serous acinus relationship: produces UBERON:0007794 ! secretion of serous gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI [Term] id: UBERON:0000410 @@ -164505,7 +164675,7 @@ is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001992 ! papillary layer of dermis relationship: RO:0002473 CL:0000057 ! composed primarily of fibroblast -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg" xsd:anyURI property_value: IAO:0000116 "consider adding grouping class for TAO:0001995 ! papilla" xsd:string [Term] @@ -164530,7 +164700,7 @@ intersection_of: has_part CL:0000319 ! mucus secreting cell relationship: capable_of GO:0070254 ! mucus secretion relationship: has_part CL:0000319 ! mucus secreting cell relationship: produces UBERON:0000912 ! mucus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI [Term] id: UBERON:0000415 @@ -164911,7 +165081,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -164947,7 +165117,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -164976,7 +165146,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -165002,7 +165172,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -165040,7 +165210,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -165095,7 +165265,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -165164,7 +165334,7 @@ xref: EHDAA2:0002007 xref: EHDAA:8146 xref: EMAPA:17972 xref: EV:0100102 -xref: FBbt:00004928 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004928 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7210 xref: GAID:396 xref: galen:Testis @@ -165189,7 +165359,7 @@ intersection_of: part_of UBERON:0000079 ! male reproductive system disjoint_from: UBERON:0000992 ! ovary disjoint_from: UBERON:0009117 ! indifferent gonad relationship: RO:0002202 UBERON:0009117 ! develops from indifferent gonad -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png" xsd:anyURI [Term] id: UBERON:0000474 @@ -165218,7 +165388,7 @@ xref: EHDAA2:0000506 xref: EHDAA:8116 xref: EMAPA:17959 xref: EV:0100110 -xref: FBbt:00004864 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004864 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45663 xref: GAID:364 xref: HAO:0000324 @@ -165237,7 +165407,7 @@ is_a: UBERON:0000990 ! reproductive system intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0003100 ! female organism -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -165263,7 +165433,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -165306,7 +165476,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -165326,7 +165496,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -165352,7 +165522,7 @@ xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 -xref: FBbt:00005835 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005835 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 @@ -165389,7 +165559,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -165424,7 +165594,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -165458,7 +165628,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -165481,7 +165651,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000484 @@ -165507,7 +165677,7 @@ xref: XAO:0004009 xref: ZFA:0001497 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0010077 ! cuboidal epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png" xsd:anyURI property_value: IAO:0000116 "needs to be synchronized with CL - there is no distinct cuboidal cell in CL" xsd:string [Term] @@ -165527,7 +165697,7 @@ xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 -xref: FBbt:00007027 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007027 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 @@ -165539,7 +165709,7 @@ xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI [Term] id: UBERON:0000486 @@ -165594,7 +165764,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000488 @@ -165780,7 +165950,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -165801,7 +165971,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -165821,7 +165991,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -165855,7 +166025,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -165873,7 +166043,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -165893,7 +166063,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -165910,8 +166080,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -165937,7 +166107,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -165954,7 +166124,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -165977,7 +166147,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -165990,7 +166160,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -166007,7 +166177,7 @@ synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 -xref: FBbt:00000123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} @@ -166060,7 +166230,7 @@ intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0004467 ! musculature of pharynx relationship: part_of UBERON:0004467 ! musculature of pharynx relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png" xsd:anyURI [Term] id: UBERON:0000939 @@ -166071,7 +166241,7 @@ comment: Though inaginal discs are sometimes described as “epithelial sacs”, subset: uberon_slim synonym: "imaginal disk" RELATED [] xref: BTO:0004658 -xref: FBbt:00001761 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001761 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MAT:0000064 xref: MIAA:0000064 xref: Wikipedia:Imaginal_disc @@ -166185,7 +166355,7 @@ relationship: capable_of GO:0001696 ! gastric acid secretion relationship: part_of UBERON:0001041 ! foregut relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:7864 {source="Wikipedia"} property_value: RO:0002161 NCBITaxon:7878 {source="Wikipedia"} property_value: RO:0002161 NCBITaxon:7955 {source="ZFA"} @@ -166268,9 +166438,9 @@ is_a: UBERON:0003519 ! thoracic cavity blood vessel is_a: UBERON:0013768 ! great vessel of heart relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system relationship: RO:0002170 UBERON:0002084 ! connected to heart left ventricle -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg" xsd:anyURI property_value: IAO:0000116 "This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae." xsd:string {source="WP"} property_value: RO:0002175 NCBITaxon:9606 @@ -166326,9 +166496,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -166351,7 +166521,7 @@ xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 -xref: FBbt:00005068 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005068 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9668 xref: GAID:439 xref: MA:0000012 @@ -166435,7 +166605,7 @@ xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 -xref: FBbt:00005095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:50801 xref: GAID:571 xref: galen:Brain @@ -166467,8 +166637,8 @@ relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous s relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -166525,8 +166695,8 @@ relationship: part_of UBERON:0005401 {source="FMA", source="MA"} ! cerebral hemi relationship: RO:0002254 UBERON:0004035 ! has developmental contribution from cortical subplate relationship: RO:0002254 UBERON:0005343 ! has developmental contribution from cortical plate relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:117569 property_value: RO:0002175 NCBITaxon:9606 @@ -166544,7 +166714,7 @@ is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: RO:0000086 PATO:0002124 ! has quality laminar -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] @@ -166608,7 +166778,7 @@ intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI [Term] id: UBERON:0000961 @@ -166639,7 +166809,7 @@ intersection_of: UBERON:0001807 ! paravertebral ganglion intersection_of: part_of UBERON:0004863 ! thoracic sympathetic nerve trunk relationship: extends_fibers_into UBERON:0018679 ! thoracic splanchnic nerve relationship: part_of UBERON:0004863 ! thoracic sympathetic nerve trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -166648,6 +166818,7 @@ name: nerve of cervical vertebra namespace: uberon def: "The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]." [Wikipedia:Cervical_nerves] comment: Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] +subset: human_reference_atlas subset: uberon_slim synonym: "cervical nerve" EXACT [FMA:5859] synonym: "cervical nerve tree" EXACT [] @@ -166665,13 +166836,14 @@ is_a: UBERON:0001780 ! spinal nerve intersection_of: UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002726 ! cervical spinal cord relationship: extends_fibers_into UBERON:0002726 ! cervical spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000963 name: head sensillum namespace: uberon -xref: FBbt:00004114 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MAT:0000204 xref: MIAA:0000204 is_a: UBERON:0002536 ! arthropod sensillum @@ -166726,7 +166898,7 @@ relationship: RO:0002202 UBERON:0004348 ! develops from optic eminence relationship: RO:0002202 UBERON:0005427 ! develops from corneal primordium relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -166826,7 +166998,7 @@ relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region relationship: RO:0002202 UBERON:0003072 {source="EHDAA2"} ! develops from optic cup -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6656 property_value: RO:0002175 NCBITaxon:9606 @@ -166848,7 +167020,7 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -166870,7 +167042,7 @@ subset: uberon_slim synonym: "omatidia" RELATED OMO:0003004 [] synonym: "omatidium" EXACT [] xref: BTO:0001922 -xref: FBbt:00004510 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004510 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000666 xref: MAT:0000143 xref: MIAA:0000143 @@ -166910,7 +167082,7 @@ is_a: UBERON:0000475 ! organism subdivision relationship: anteriorly_connected_to UBERON:0000033 ! head relationship: part_of UBERON:0000153 ! anterior region of body relationship: posteriorly_connected_to UBERON:0002100 ! trunk -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg" xsd:anyURI [Term] id: UBERON:0000975 @@ -166947,7 +167119,7 @@ relationship: RO:0002170 UBERON:0007831 ! connected to pectoral girdle skeleton relationship: RO:0002170 UBERON:0008255 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to right clavicle relationship: RO:0002170 UBERON:0008256 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to left clavicle relationship: RO:0002433 UBERON:0003252 ! contributes to morphology of thoracic rib cage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg" xsd:anyURI property_value: IAO:0000116 "in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum" xsd:string property_value: RO:0002161 NCBITaxon:8570 {source="Wikipedia"} property_value: RO:0002175 NCBITaxon:9606 @@ -166990,7 +167162,7 @@ intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: overlaps UBERON:0001470 ! glenohumeral joint relationship: proximally_connected_to UBERON:0007831 ! pectoral girdle skeleton relationship: RO:0002202 UBERON:0006245 ! develops from humerus cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -167030,7 +167202,7 @@ relationship: RO:0000086 PATO:0001748 ! has quality invaginated relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:8782 {source="ISBN:978-0030223693", source="https://orcid.org/0000-0003-3308-6245"} [Term] @@ -167094,7 +167266,7 @@ intersection_of: UBERON:0015004 ! tibia endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: BSPO:0001113 UBERON:0010720 ! hindlimb zeugopod skeleton relationship: RO:0002202 UBERON:0010849 ! develops from tibia cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -167143,7 +167315,7 @@ relationship: RO:0002170 UBERON:0000979 {gci_relation="part_of", gci_filler="NCB relationship: RO:0002170 UBERON:0001272 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to innominate bone relationship: RO:0002170 UBERON:0002446 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to patella relationship: RO:0002202 UBERON:0010129 ! develops from femur cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -167239,7 +167411,7 @@ intersection_of: RO:0002179 UBERON:0009472 ! drains axilla relationship: part_of UBERON:0001467 ! shoulder relationship: RO:0002170 UBERON:0001587 ! connected to subclavian vein relationship: RO:0002179 UBERON:0009472 ! drains axilla -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -167286,7 +167458,7 @@ relationship: part_of UBERON:0002298 ! brainstem relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002433 UBERON:0001895 ! contributes to morphology of metencephalon relationship: RO:0002433 UBERON:0002298 ! contributes to morphology of brainstem -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png" xsd:anyURI property_value: IAO:0000116 "The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -167325,7 +167497,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0008811 {source="Wikipedia"} ! intromittent organ relationship: RO:0002202 UBERON:0004876 {source="Wikipedia"} ! develops from urogenital fold relationship: RO:0002202 UBERON:0005876 {source="EHDAA2"} ! develops from undifferentiated genital tubercle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg" xsd:anyURI [Term] id: UBERON:0000990 @@ -167356,7 +167528,7 @@ xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 -xref: FBbt:00004857 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004857 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 @@ -167394,10 +167566,10 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0022414 ! reproductive process relationship: has_part UBERON:0000991 ! gonad relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://purl.org/dc/terms/date "2022-06-10T18:22:34Z" xsd:dateTime -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI property_value: IAO:0000116 "consider splitting genitalia from reproductive system" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-10T18:22:34Z" xsd:dateTime [Term] id: UBERON:0000991 @@ -167484,7 +167656,7 @@ xref: EHDAA2:0001360 xref: EHDAA:8124 xref: EMAPA:17962 xref: EV:0100111 -xref: FBbt:00004865 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004865 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7209 xref: GAID:367 xref: MA:0000384 @@ -167506,8 +167678,8 @@ disjoint_from: UBERON:0009117 ! indifferent gonad relationship: BSPO:0000126 UBERON:0003975 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA-abduced-lr"} ! internal female genitalia relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: RO:0002202 UBERON:0009117 ! develops from indifferent gonad -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -167581,9 +167753,9 @@ is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct relationship: part_of UBERON:0004175 ! internal genitalia relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria relationship: RO:0002495 UBERON:0005795 ! immediate transformation of embryonic uterus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -167619,8 +167791,8 @@ is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct relationship: part_of UBERON:0003975 {source="FMA"} ! internal female genitalia relationship: RO:0002202 UBERON:0000164 {source="Wikipedia"} ! develops from primitive urogenital sinus relationship: RO:0002433 UBERON:0003975 ! contributes to morphology of internal female genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg" xsd:anyURI [Term] id: UBERON:0000997 @@ -167659,7 +167831,7 @@ is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0005056 ! external female genitalia relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg" xsd:anyURI [Term] id: UBERON:0000998 @@ -167704,8 +167876,8 @@ relationship: part_of UBERON:0000473 ! testis relationship: produces UBERON:0010143 ! seminal vesicle fluid relationship: RO:0002202 UBERON:0000080 ! develops from mesonephros relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI [Term] id: UBERON:0000999 @@ -167742,8 +167914,8 @@ relationship: channels_from UBERON:0000998 ! seminal vesicle relationship: channels_from UBERON:0001000 ! vas deferens relationship: channels_into UBERON:0000057 ! urethra relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI [Term] id: UBERON:0001000 @@ -167784,7 +167956,7 @@ relationship: part_of UBERON:0005352 {source="FMA"} ! spermatic cord relationship: part_of UBERON:0006947 ! male genital duct relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI [Term] id: UBERON:0001003 @@ -167887,12 +168059,12 @@ relationship: capable_of GO:0003016 ! respiratory system process relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -167931,7 +168103,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -167995,7 +168167,7 @@ xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 -xref: FBbt:00005056 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005056 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract @@ -168051,7 +168223,7 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -168138,7 +168310,7 @@ is_a: BFO:0000002 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -168164,7 +168336,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -168200,8 +168372,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -168232,7 +168404,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -168271,7 +168443,7 @@ synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 -xref: FBbt:00005100 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005100 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle @@ -168327,7 +168499,7 @@ xref: EHDAA:4657 xref: EMAPA:32808 xref: EMAPA:32815 xref: EV:0100371 -xref: FBbt:00005105 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005105 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:65132 xref: FMA:65239 xref: GAID:747 @@ -168366,7 +168538,7 @@ synonym: "afferent nerve" RELATED [] synonym: "nervus sensorius" EXACT OMO:0003011 [Wikipedia:Sensory_nerve] xref: AEO:0000201 xref: EHDAA2:0003200 -xref: FBbt:00005136 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5868 xref: Wikipedia:Sensory_nerve is_a: UBERON:0001021 ! nerve @@ -168395,7 +168567,7 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007692 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -168411,7 +168583,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001033 @@ -168495,7 +168667,7 @@ relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia relationship: RO:0002202 UBERON:0002073 ! develops from hair follicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png" xsd:anyURI property_value: IAO:0000116 "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)" xsd:string [Term] @@ -168510,7 +168682,7 @@ subset: uberon_slim synonym: "ch" RELATED [] synonym: "scolopophorous organ" RELATED [] xref: EFO:0000940 -xref: FBbt:00005215 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005215 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MAT:0000209 xref: MIAA:0000209 xref: Wikipedia:Chordotonal_organ @@ -168547,7 +168719,7 @@ is_a: UBERON:0005631 {seeAlso="https://github.com/obophenotype/uberon/issues/635 is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac relationship: RO:0002254 UBERON:0000925 {source="ISBN:0073040584"} ! has developmental contribution from endoderm relationship: RO:0002254 UBERON:0004872 {source="ISBN:0073040584"} ! has developmental contribution from splanchnic layer of lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png" xsd:anyURI property_value: IAO:0000116 "consider splitting class" xsd:string [Term] @@ -168566,7 +168738,7 @@ xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 -xref: FBbt:00005379 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005379 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 @@ -168577,7 +168749,7 @@ xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string [Term] @@ -168666,7 +168838,7 @@ is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0004908 ! upper digestive tract relationship: proximally_connected_to UBERON:0001042 ! chordate pharynx relationship: RO:0002202 UBERON:0001041 ! develops from foregut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -168688,7 +168860,7 @@ xref: EHDAA2:0001775 xref: EHDAA:7987 xref: EMAPA:17751 xref: EV:0100059 -xref: FBbt:00005382 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005382 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9597 xref: GAID:937 xref: galen:SalivaryGland @@ -168709,7 +168881,7 @@ relationship: produces UBERON:0001836 ! saliva relationship: RO:0001025 UBERON:0000167 ! located in oral cavity relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI [Term] id: UBERON:0001045 @@ -168727,7 +168899,7 @@ xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 -xref: FBbt:00005383 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005383 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 @@ -168739,7 +168911,7 @@ xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string [Term] @@ -168757,7 +168929,7 @@ xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 -xref: FBbt:00005384 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005384 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 @@ -168771,7 +168943,7 @@ is_a: BFO:0000002 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001045 ! midgut relationship: RO:0002202 UBERON:0003104 {source="Wikipedia"} ! develops from mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string [Term] @@ -168791,7 +168963,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -168838,7 +169010,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001052 @@ -168881,9 +169053,9 @@ relationship: part_of UBERON:0006866 ! terminal part of digestive tract relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region relationship: RO:0002150 UBERON:0001159 ! continuous with sigmoid colon relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -168899,7 +169071,7 @@ synonym: "Malpighian tube" RELATED [UBERON:cjm] synonym: "tuba Malpighii" RELATED [BTO:0000810] xref: BTO:0000810 xref: EFO:0000243 -xref: FBbt:00005786 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005786 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:1228 xref: MAT:0000123 xref: MESH:D008317 @@ -168922,7 +169094,7 @@ synonym: "corpora pedunculata" RELATED [FBbt:00005801, PMID:21062451] synonym: "mushroom bodies" EXACT OMO:0003004 [] xref: BTO:0002675 xref: EFO:0000925 -xref: FBbt:00005801 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005801 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:1231 xref: MAT:0000336 xref: MESH:D024521 @@ -168952,7 +169124,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -169005,7 +169177,7 @@ relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0004913 ! hepatopancreatic ampulla relationship: RO:0002150 UBERON:0001174 ! continuous with common bile duct relationship: RO:0002202 UBERON:0003924 {source="EHDAA2"} ! develops from ventral pancreatic bud -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -169037,7 +169209,7 @@ is_a: UBERON:0011135 ! intervertebral cartilage intersection_of: UBERON:0011135 ! intervertebral cartilage intersection_of: has_part UBERON:0002242 ! nucleus pulposus relationship: has_part UBERON:0002242 ! nucleus pulposus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png" xsd:anyURI [Term] id: UBERON:0001068 @@ -169092,7 +169264,7 @@ is_a: UBERON:0005396 {source="MA"} ! carotid artery segment relationship: part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches relationship: RO:0002202 UBERON:0001530 {source="EHDAA2"} ! develops from common carotid artery plus branches relationship: RO:0002380 UBERON:0001530 {source="FMA"} ! branching part of common carotid artery plus branches -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722" xsd:anyURI @@ -169121,7 +169293,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001072 -name: posterior vena cava +name: inferior vena cava namespace: uberon def: "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Inferior_vena_cava] subset: human_reference_atlas @@ -169129,9 +169301,8 @@ subset: pheno_slim subset: uberon_slim synonym: "caudal vena cava" RELATED [VHOG:0001194] synonym: "inferior caval vein" EXACT [http://orcid.org/0000-0002-6601-2165] -synonym: "inferior vena cava" EXACT [Wikipedia:Venae_cavae] synonym: "postcava" RELATED [] -synonym: "posterior vena cava" EXACT [Wikipedia:Venae_cavae] +synonym: "posterior vena cava" EXACT [PMID:21154280] synonym: "vena cava inferior" RELATED OMO:0003011 [BTO:0002682, Wikipedia:Inferior_vena_cava] xref: AAO:0011083 xref: BTO:0002682 @@ -169156,7 +169327,7 @@ relationship: channels_into UBERON:0002078 {gci_relation="part_of", gci_filler=" relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -169247,7 +169418,7 @@ is_a: UBERON:0016491 ! vertebral centrum element intersection_of: UBERON:0016491 ! vertebral centrum element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: part_of UBERON:0002412 ! vertebra -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png" xsd:anyURI [Term] id: UBERON:0001076 @@ -169276,7 +169447,7 @@ xref: Wikipedia:Spinous_process xref: ZFA:0001336 is_a: UBERON:0006061 ! process of vertebra relationship: part_of UBERON:0003861 ! neural arch -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png" xsd:anyURI [Term] id: UBERON:0001077 @@ -169298,7 +169469,7 @@ xref: SCTID:264238006 xref: Wikipedia:Transverse_process xref: XAO:0003102 is_a: UBERON:0006061 ! process of vertebra -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG" xsd:anyURI [Term] id: UBERON:0001081 @@ -169561,7 +169732,7 @@ relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITa relationship: RO:0002254 UBERON:0000930 {source="XAO-modified"} ! has developmental contribution from stomodeum relationship: RO:0002254 UBERON:0005176 {source="ZFA-modified"} ! has developmental contribution from tooth enamel organ relationship: RO:0002495 UBERON:0008281 {source="cjm"} ! immediate transformation of tooth bud -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg" xsd:anyURI property_value: RO:0002161 NCBITaxon:189497 {source="Wikipedia"} property_value: RO:0002161 NCBITaxon:8782 property_value: RO:0002161 NCBITaxon:9257 {source="PMID:10210685"} @@ -169731,7 +169902,7 @@ xref: Wikipedia:Pectoralis_minor_muscle is_a: UBERON:0001495 {source="FMA"} ! pectoral muscle relationship: RO:0002372 UBERON:0002228 ! has muscle origin rib relationship: RO:0002373 UBERON:0007174 ! has muscle insertion medial border of scapula -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5d/Pectoralis_minor.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5d/Pectoralis_minor.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -169806,7 +169977,7 @@ relationship: overlaps UBERON:0001469 {gci_relation="part_of", gci_filler="NCBIT relationship: RO:0002170 UBERON:0000975 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sternum relationship: RO:0002202 UBERON:0010905 ! develops from clavicle bone primordium relationship: RO:0002254 UBERON:0010843 ! has developmental contribution from clavicle cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -169845,7 +170016,7 @@ relationship: RO:0002372 UBERON:0007175 ! has muscle origin inferior angle of sc relationship: RO:0002373 UBERON:0000976 ! has muscle insertion humerus relationship: RO:0002568 UBERON:0001476 {source="dbpedia"} ! has muscle antagonist deltoid relationship: RO:0002568 UBERON:0002380 {source="dbpedia"} ! has muscle antagonist trapezius muscle -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -169896,9 +170067,9 @@ xref: VHOG:0001424 xref: Wikipedia:Right_lobe_of_liver xref: ZFA:0005173 is_a: UBERON:0001113 ! lobe of liver -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0001115 @@ -169925,9 +170096,9 @@ xref: VHOG:0001423 xref: Wikipedia:Left_lobe_of_liver xref: ZFA:0005172 is_a: UBERON:0001113 ! lobe of liver -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0001118 @@ -169956,7 +170127,7 @@ intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: BSPO:0000126 UBERON:0002046 {source="FMA-abduced-lr"} ! thyroid gland relationship: part_of UBERON:0002046 ! thyroid gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI [Term] id: UBERON:0001119 @@ -170031,7 +170202,7 @@ relationship: RO:0002202 UBERON:0010986 {source="EHDAA2"} ! develops from serrat relationship: RO:0002372 UBERON:0002228 ! has muscle origin rib relationship: RO:0002373 UBERON:0006849 ! has muscle insertion scapula relationship: RO:0002568 UBERON:0002380 {source="dbpedia"} ! has muscle antagonist trapezius muscle -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c6/Serratus_anterior.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c6/Serratus_anterior.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170108,7 +170279,7 @@ relationship: part_of UBERON:0006692 ! vertebral canal relationship: part_of UBERON:0010913 ! vertebral element relationship: RO:0002570 UBERON:0002240 ! conduit for spinal cord relationship: RO:0002571 UBERON:0010913 ! lumen of vertebral element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png" xsd:anyURI [Term] id: UBERON:0001132 @@ -170223,7 +170394,7 @@ intersection_of: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle f relationship: part_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: RO:0002202 UBERON:0003082 ! develops from myotome relationship: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string [Term] @@ -170273,7 +170444,7 @@ disjoint_from: UBERON:0002036 ! striated muscle tissue relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber relationship: RO:0002473 CL:0000192 ! composed primarily of smooth muscle cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI [Term] id: UBERON:0001136 @@ -170305,7 +170476,7 @@ intersection_of: part_of UBERON:0000042 ! serous membrane intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm relationship: part_of UBERON:0000042 ! serous membrane relationship: RO:0002473 CL:0000077 {source="FMA"} ! composed primarily of mesothelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI [Term] id: UBERON:0001137 @@ -170330,7 +170501,7 @@ xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] id: UBERON:0001138 @@ -170359,7 +170530,7 @@ relationship: part_of UBERON:0005806 ! portal system relationship: RO:0002170 UBERON:0001639 ! connected to hepatic portal vein relationship: RO:0002179 UBERON:0002108 ! drains small intestine relationship: RO:0002202 UBERON:0005487 {source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170381,10 +170552,10 @@ xref: UMLS:C0226758 {source="ncithesaurus:Common_Iliac_Vein"} xref: Wikipedia:Common_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein is_a: UBERON:0015212 ! lateral structure -relationship: BSPO:0000126 UBERON:0001072 {source="FMA-abduced-lr"} ! posterior vena cava -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI +relationship: BSPO:0000126 UBERON:0001072 {source="FMA-abduced-lr"} ! inferior vena cava +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170416,10 +170587,10 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002179 UBERON:0002113 ! drains kidney -relationship: RO:0002376 UBERON:0001072 ! tributary of posterior vena cava -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002376 UBERON:0001072 ! tributary of inferior vena cava +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170439,8 +170610,8 @@ is_a: UBERON:0001140 ! renal vein intersection_of: UBERON:0001140 ! renal vein intersection_of: RO:0002179 UBERON:0004539 ! drains right kidney relationship: RO:0002179 UBERON:0004539 ! drains right kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170460,9 +170631,9 @@ is_a: UBERON:0001140 ! renal vein intersection_of: UBERON:0001140 ! renal vein intersection_of: RO:0002179 UBERON:0004538 ! drains left kidney relationship: RO:0002179 UBERON:0004538 ! drains left kidney -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170500,8 +170671,8 @@ disjoint_from: UBERON:0001639 ! hepatic portal vein relationship: part_of UBERON:0006877 ! vasculature of liver relationship: RO:0002179 UBERON:0002107 ! drains liver relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein -relationship: RO:0002376 UBERON:0001072 {source="FMA-abduced-lr"} ! tributary of posterior vena cava -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI +relationship: RO:0002376 UBERON:0001072 {source="FMA-abduced-lr"} ! tributary of inferior vena cava +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI property_value: IAO:0000116 "todo - add developmental relationships for other taxa" xsd:string [Term] @@ -170533,11 +170704,11 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0000473 ! drains testis relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism -relationship: RO:0002170 UBERON:0001072 ! connected to posterior vena cava +relationship: RO:0002170 UBERON:0001072 ! connected to inferior vena cava relationship: RO:0002170 UBERON:0001330 ! connected to pampiniform plexus relationship: RO:0002179 UBERON:0000473 ! drains testis relationship: sexually_homologous_to UBERON:0001145 ! ovarian vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png" xsd:anyURI property_value: IAO:0000116 "TODO - check testicular vs spermatic vein (MA:0002218)" xsd:string [Term] @@ -170571,7 +170742,7 @@ intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0000992 ! drains ovary relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism relationship: RO:0002179 UBERON:0000992 ! drains ovary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg" xsd:anyURI [Term] id: UBERON:0001146 @@ -170593,7 +170764,7 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0002369 ! drains adrenal gland relationship: RO:0002179 UBERON:0002369 ! drains adrenal gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI [Term] id: UBERON:0001152 @@ -170628,8 +170799,8 @@ relationship: channels_into UBERON:0001174 ! common bile duct relationship: RO:0002150 UBERON:0001174 ! continuous with common bile duct relationship: RO:0002150 UBERON:0002110 ! continuous with gallbladder relationship: RO:0002202 UBERON:0005604 {source="EHDAA2"} ! develops from extrahepatic part of hepatic duct -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI [Term] id: UBERON:0001153 @@ -170675,9 +170846,9 @@ relationship: RO:0002150 UBERON:0001156 {source="Wikipedia"} ! continuous with a relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:32443 {source="Wikipedia"} property_value: RO:0002175 NCBITaxon:9606 @@ -170722,9 +170893,9 @@ is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0000059 ! large intestine relationship: RO:0002150 UBERON:0001153 {xref="http://orcid.org/0000-0002-1572-1316"} ! continuous with caecum relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:40674 property_value: RO:0002175 NCBITaxon:9606 @@ -170795,9 +170966,9 @@ is_a: BFO:0000002 is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: RO:0002150 UBERON:0001157 ! continuous with transverse colon relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170826,9 +170997,9 @@ is_a: BFO:0000002 is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: RO:0002150 UBERON:0001158 ! continuous with descending colon relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170857,9 +171028,9 @@ is_a: BFO:0000002 is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: RO:0002150 UBERON:0001159 ! continuous with sigmoid colon relationship: RO:0002202 UBERON:0001046 {source="Wikipedia"} ! develops from hindgut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170893,9 +171064,9 @@ is_a: BFO:0000002 is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon relationship: RO:0002150 UBERON:0001052 ! continuous with rectum relationship: RO:0002202 UBERON:0001046 {source="Wikipedia"} ! develops from hindgut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -170932,7 +171103,7 @@ is_a: BFO:0000002 is_a: UBERON:0009870 ! zone of stomach relationship: has_part UBERON:0010038 ! fundic gastric gland relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI [Term] id: UBERON:0001161 @@ -170957,7 +171128,7 @@ xref: SCTID:362140009 xref: UMLS:C0227230 {source="ncithesaurus:Body_of_Stomach"} xref: Wikipedia:Body_of_stomach is_a: UBERON:0009870 {source="FMA"} ! zone of stomach -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI property_value: IAO:0000116 "we include this as zone of stomach even though it is not distinguished by gland type" xsd:string [Term] @@ -170995,7 +171166,7 @@ relationship: RO:0002150 UBERON:0001043 ! continuous with esophagus relationship: RO:0002150 UBERON:0001161 ! continuous with body of stomach relationship: RO:0002160 NCBITaxon:40674 {source="ISBN:0073040584"} ! only in taxon Mammalia relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI property_value: IAO:0000116 "There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]" xsd:string property_value: IAO:0000116 "We follow Kardong in defining stomach regions by glands." xsd:string @@ -171034,7 +171205,7 @@ relationship: has_part CL:0000508 ! type G enteroendocrine cell relationship: part_of UBERON:0001166 {source="Wikipedia"} ! pylorus relationship: RO:0002150 UBERON:0001161 ! continuous with body of stomach relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI [Term] id: UBERON:0001166 @@ -171073,7 +171244,7 @@ relationship: has_part UBERON:0001165 ! pyloric antrum relationship: has_part UBERON:0008858 ! pyloric canal relationship: has_part UBERON:0008861 ! pyloric gastric gland relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI property_value: IAO:0000116 "We follow Kardong in defining stomach regions by glands" xsd:string [Term] @@ -171255,7 +171426,7 @@ is_a: UBERON:0003703 ! extrahepatic bile duct relationship: channels_into UBERON:0001064 ! ventral pancreatic duct relationship: RO:0002150 UBERON:0001152 ! continuous with cystic duct relationship: RO:0002150 UBERON:0001175 ! continuous with common hepatic duct -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171283,7 +171454,7 @@ relationship: part_of UBERON:0005604 {source="MA"} ! extrahepatic part of hepati relationship: RO:0002150 UBERON:0001176 {source="Wikipedia"} ! continuous with right hepatic duct relationship: RO:0002150 UBERON:0001177 {source="Wikipedia"} ! continuous with left hepatic duct relationship: RO:0002495 UBERON:0010081 ! immediate transformation of future common hepatic duct -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part" xsd:string [Term] @@ -171347,7 +171518,7 @@ is_a: UBERON:0022350 ! visceral serous membrane intersection_of: UBERON:0022350 ! visceral serous membrane intersection_of: part_of UBERON:0002358 ! peritoneum relationship: part_of UBERON:0002358 ! peritoneum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI [Term] id: UBERON:0001179 @@ -171413,10 +171584,10 @@ intersection_of: RO:0002178 UBERON:0002115 ! supplies jejunum intersection_of: RO:0002178 UBERON:0002116 ! supplies ileum relationship: RO:0002178 UBERON:0002115 ! supplies jejunum relationship: RO:0002178 UBERON:0002116 ! supplies ileum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171452,9 +171623,9 @@ intersection_of: RO:0002178 UBERON:0001158 ! supplies descending colon intersection_of: RO:0002178 UBERON:0001159 ! supplies sigmoid colon relationship: RO:0002178 UBERON:0001158 ! supplies descending colon relationship: RO:0002178 UBERON:0001159 ! supplies sigmoid colon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171493,9 +171664,9 @@ is_a: UBERON:0012254 ! abdominal aorta artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0002113 ! supplies kidney relationship: RO:0002178 UBERON:0002113 ! supplies kidney -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: IAO:0000116 "renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -171519,9 +171690,9 @@ is_a: UBERON:0001184 ! renal artery intersection_of: UBERON:0001184 ! renal artery intersection_of: RO:0002178 UBERON:0004539 ! supplies right kidney relationship: RO:0002178 UBERON:0004539 ! supplies right kidney -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171543,8 +171714,8 @@ is_a: UBERON:0001184 ! renal artery intersection_of: UBERON:0001184 ! renal artery intersection_of: RO:0002178 UBERON:0004538 ! supplies left kidney relationship: RO:0002178 UBERON:0004538 ! supplies left kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171573,7 +171744,7 @@ is_a: UBERON:0010192 ! genital artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0000473 ! supplies testis relationship: RO:0002178 UBERON:0000473 ! supplies testis -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171639,7 +171810,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0000992 ! supplies ovary relationship: RO:0002170 UBERON:0001516 ! connected to abdominal aorta relationship: RO:0002178 UBERON:0000992 ! supplies ovary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171663,7 +171834,7 @@ xref: UMLS:C1261084 {source="ncithesaurus:Common_Iliac_Artery"} xref: Wikipedia:Common_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery is_a: UBERON:0012254 ! abdominal aorta artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171692,7 +171863,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0002107 ! supplies liver relationship: RO:0002178 UBERON:0002107 ! supplies liver -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171722,9 +171893,9 @@ intersection_of: RO:0002178 UBERON:0002106 ! supplies spleen disjoint_from: UBERON:0001640 ! celiac artery relationship: RO:0002178 UBERON:0002106 ! supplies spleen relationship: RO:0002252 UBERON:0001640 ! connecting branch of celiac artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/268" xsd:anyURI @@ -171750,9 +171921,9 @@ intersection_of: RO:0002178 UBERON:0001157 ! supplies transverse colon intersection_of: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery relationship: RO:0002178 UBERON:0001157 ! supplies transverse colon relationship: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171781,9 +171952,9 @@ relationship: RO:0002178 UBERON:0001153 ! supplies caecum relationship: RO:0002178 UBERON:0001154 ! supplies vermiform appendix relationship: RO:0002178 UBERON:0002116 ! supplies ileum relationship: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -171832,7 +172003,7 @@ intersection_of: part_of UBERON:0000945 ! stomach relationship: capable_of GO:0001696 ! gastric acid secretion relationship: part_of UBERON:0001167 ! wall of stomach relationship: RO:0002433 UBERON:0001167 ! contributes to morphology of wall of stomach -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg" xsd:anyURI [Term] id: UBERON:0001200 @@ -172202,7 +172373,7 @@ is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: has_part UBERON:0001981 ! blood vessel relationship: has_part UBERON:0012425 ! striated border microvillus layer relationship: part_of UBERON:0001277 {source="ZFA"} ! intestinal epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI property_value: IAO:0000116 "in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine" xsd:string [Term] @@ -172230,8 +172401,8 @@ intersection_of: UBERON:0005617 ! mesenteric vein intersection_of: RO:0002179 UBERON:0000059 ! drains large intestine relationship: RO:0002179 UBERON:0000059 ! drains large intestine relationship: RO:0002376 UBERON:0003713 {source="FMA/obol"} ! tributary of splenic vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172250,7 +172421,7 @@ intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0002115 ! drains jejunum relationship: RO:0002179 UBERON:0002115 ! drains jejunum relationship: RO:0002376 UBERON:0001138 {source="FMA/obol"} ! tributary of superior mesenteric vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172293,9 +172464,9 @@ intersection_of: RO:0002179 UBERON:0001157 ! drains transverse colon intersection_of: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein relationship: RO:0002179 UBERON:0001157 ! drains transverse colon relationship: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172321,9 +172492,9 @@ intersection_of: RO:0002179 UBERON:0002116 ! drains ileum intersection_of: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein relationship: RO:0002179 UBERON:0001153 ! drains caecum relationship: RO:0002179 UBERON:0001155 ! drains colon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172341,8 +172512,8 @@ is_a: UBERON:0000056 ! ureter intersection_of: UBERON:0000056 ! ureter intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_R.glb" xsd:anyURI [Term] id: UBERON:0001223 @@ -172359,8 +172530,8 @@ is_a: UBERON:0000056 ! ureter intersection_of: UBERON:0000056 ! ureter intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_L.glb" xsd:anyURI [Term] id: UBERON:0001224 @@ -172396,7 +172567,7 @@ relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter relationship: RO:0002150 UBERON:0000056 {source="FMA"} ! continuous with ureter relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172427,11 +172598,11 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172457,11 +172628,11 @@ is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001294 ! inner medulla of kidney relationship: RO:0002433 UBERON:0001224 ! contributes to morphology of renal pelvis -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172499,7 +172670,7 @@ relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -172543,7 +172714,7 @@ relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} ! glomerular fi relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002202 UBERON:0004199 ! develops from S-shaped body relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI [Term] id: UBERON:0001231 @@ -172701,7 +172872,7 @@ relationship: capable_of GO:0006705 ! mineralocorticoid biosynthetic process relationship: capable_of GO:0035932 ! aldosterone secretion relationship: part_of UBERON:0002369 ! adrenal gland relationship: RO:0002433 UBERON:0002369 ! contributes to morphology of adrenal gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI [Term] id: UBERON:0001236 @@ -172747,7 +172918,7 @@ relationship: has_part CL:0002083 {source="FMA"} ! type I cell of adrenal medull relationship: part_of UBERON:0002369 ! adrenal gland relationship: RO:0002219 UBERON:0001235 {source="Wikipedia"} ! surrounded by adrenal cortex relationship: RO:0002433 UBERON:0002369 ! contributes to morphology of adrenal gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI [Term] id: UBERON:0001237 @@ -172771,7 +172942,7 @@ xref: SCTID:276159005 xref: UMLS:C0442134 {source="ncithesaurus:Paraaortic"} xref: Wikipedia:Organ_of_Zuckerkandl is_a: UBERON:0012279 ! chromaffin paraganglion -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI [Term] id: UBERON:0001238 @@ -172938,7 +173109,7 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00047153 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00047153 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -172957,8 +173128,8 @@ intersection_of: BSPO:0001108 UBERON:0001555 ! digestive tract relationship: BSPO:0001108 UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract relationship: RO:0002202 UBERON:0000931 ! develops from proctodeum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173007,8 +173178,8 @@ intersection_of: RO:0002371 UBERON:0002107 ! attached to liver relationship: part_of UBERON:0005626 {source="MA"} ! ventral mesogastrium relationship: RO:0002371 UBERON:0000309 ! attached to body wall relationship: RO:0002371 UBERON:0002107 ! attached to liver -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0001249 @@ -173065,7 +173236,7 @@ xref: Wikipedia:Red_pulp is_a: UBERON:1000023 ! spleen pulp relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen relationship: RO:0002473 CL:0000542 ! composed primarily of lymphocyte -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} property_value: RO:0002175 NCBITaxon:9606 @@ -173091,7 +173262,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: adjacent_to UBERON:0001250 ! red pulp of spleen relationship: adjacent_to UBERON:0001959 ! white pulp of spleen relationship: part_of UBERON:0002106 ! spleen -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173201,9 +173372,9 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173264,9 +173435,9 @@ is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0006082 ! fundus of urinary bladder relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Illu_bladder.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Illu_bladder.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173297,7 +173468,7 @@ intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png" xsd:anyURI [Term] id: UBERON:0001259 @@ -173485,9 +173656,9 @@ relationship: has_part UBERON:0000017 {gci_relation="part_of", gci_filler="NCBIT relationship: RO:0002160 NCBITaxon:7742 {source="PMID:16417468"} ! only in taxon Vertebrata relationship: RO:0002254 UBERON:0003923 {source="Wikipedia"} ! has developmental contribution from dorsal pancreatic bud relationship: RO:0002254 UBERON:0003924 {source="Wikipedia"} ! has developmental contribution from ventral pancreatic bud -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173604,7 +173775,7 @@ is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001464 {source="FMA"} ! hip -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png" xsd:anyURI property_value: IAO:0000116 "currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -173645,8 +173816,8 @@ relationship: BSPO:0000126 UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001272 {source="FMA"} ! innominate bone relationship: RO:0002202 UBERON:0010714 {source="cjm"} ! develops from iliac cartilage element relationship: RO:0002433 UBERON:0007830 ! contributes to morphology of pelvic girdle bone/zone -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:32443 {source="Wikipedia"} [Term] @@ -173682,9 +173853,9 @@ relationship: BSPO:0000126 UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001272 ! innominate bone relationship: RO:0002202 UBERON:0006254 {source="cjm"} ! develops from ischial cartilage element relationship: RO:0002433 UBERON:0007830 ! contributes to morphology of pelvic girdle bone/zone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI [Term] id: UBERON:0001276 @@ -173794,7 +173965,7 @@ relationship: has_part UBERON:0002017 ! portal vein relationship: has_part UBERON:0003704 ! intrahepatic bile duct relationship: part_of UBERON:0001172 ! hepatic acinus relationship: RO:0002433 UBERON:0001171 ! contributes to morphology of portal lobule -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -173933,7 +174104,7 @@ relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney relationship: RO:0002495 UBERON:0010532 {source="Bgee:AN"} ! immediate transformation of primitive nephron -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -174008,7 +174179,7 @@ relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerul relationship: RO:0002150 UBERON:0001290 ! continuous with proximal straight tubule relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI [Term] id: UBERON:0001288 @@ -174039,7 +174210,7 @@ intersection_of: RO:0002150 UBERON:0001292 ! continuous with distal convoluted t relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule relationship: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string property_value: RO:0002175 NCBITaxon:8782 @@ -174064,7 +174235,7 @@ xref: Wikipedia:Descending_limb_of_loop_of_henle is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174129,7 +174300,7 @@ xref: Wikipedia:Thick_ascending_limb_of_loop_of_Henle is_a: UBERON:0009035 {source="MA"} ! renal straight tubule relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle relationship: RO:0002433 UBERON:0005164 ! contributes to morphology of ascending limb of loop of Henle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -174160,7 +174331,7 @@ is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0004135 {source="EMAPA", source="GO", source="MA-modified-from-isa"} ! distal tubule relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174248,7 +174419,7 @@ intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174283,7 +174454,7 @@ relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall relationship: RO:0002219 UBERON:0001297 ! surrounded by serosa of uterus relationship: RO:0002221 UBERON:0001295 ! surrounds endometrium relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI [Term] id: UBERON:0001297 @@ -174311,7 +174482,7 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000459 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! uterine wall -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - check for parallel structure with peritoneum" xsd:string [Term] @@ -174342,8 +174513,8 @@ relationship: part_of UBERON:0000989 ! penis relationship: RO:0002433 UBERON:0000989 ! contributes to morphology of penis relationship: RO:0002495 UBERON:0013239 {source="Bgee:AN"} ! immediate transformation of future glans penis relationship: sexually_homologous_to UBERON:0006653 ! glans clitoris -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI [Term] id: UBERON:0001301 @@ -174380,7 +174551,7 @@ relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003074 {source="Wikipedia"} ! develops from mesonephric duct relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg" xsd:anyURI property_value: IAO:0000116 "Kardong has epididymis in elasmobranch" xsd:string [Term] @@ -174400,7 +174571,7 @@ is_a: UBERON:0003889 ! fallopian tube intersection_of: UBERON:0003889 ! fallopian tube intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_R.glb" xsd:anyURI [Term] id: UBERON:0001303 @@ -174419,7 +174590,7 @@ is_a: UBERON:0003889 ! fallopian tube intersection_of: UBERON:0003889 ! fallopian tube intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_L.glb" xsd:anyURI [Term] id: UBERON:0001304 @@ -174487,8 +174658,8 @@ relationship: has_part CL:0000023 ! oocyte relationship: has_part CL:0002174 ! follicular cell of ovary relationship: has_part UBERON:0000038 ! follicular fluid relationship: RO:0002202 UBERON:0005296 {source="Wikipedia"} ! develops from ovary sex cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI property_value: IAO:0000116 "TODO - align subtypes based on staging, which is taxon-specific" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -174533,7 +174704,7 @@ xref: UMLS:C0226398 {source="ncithesaurus:External_Iliac_Artery"} xref: Wikipedia:External_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery relationship: part_of UBERON:0001191 ! common iliac artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray539.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray539.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174556,7 +174727,7 @@ xref: UMLS:C0226364 {source="ncithesaurus:Internal_Iliac_Artery"} xref: Wikipedia:Internal_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery relationship: part_of UBERON:0001191 ! common iliac artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d3/Iliac_artery_bifurcation.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d3/Iliac_artery_bifurcation.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174585,8 +174756,8 @@ xref: UMLS:C0041632 {source="ncithesaurus:Umbilical_Artery"} xref: Wikipedia:Umbilical_artery is_a: UBERON:0001637 ! artery is_a: UBERON:0010260 ! umbilical blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI property_value: IAO:0000116 "todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships" xsd:string property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/328" xsd:anyURI @@ -174616,7 +174787,7 @@ relationship: RO:0002178 UBERON:0001000 {gci_filler="UBERON:0003101", gci_relati relationship: RO:0002178 UBERON:0002367 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies prostate gland relationship: RO:0002178 UBERON:0006082 ! supplies fundus of urinary bladder relationship: RO:0002252 UBERON:0001309 ! connecting branch of internal iliac artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174641,7 +174812,7 @@ is_a: UBERON:0009027 ! vesical artery intersection_of: UBERON:0009027 ! vesical artery intersection_of: RO:0002178 UBERON:0000056 ! supplies ureter relationship: RO:0002252 UBERON:0001310 ! connecting branch of umbilical artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174664,8 +174835,8 @@ xref: Wikipedia:External_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein relationship: RO:0002170 UBERON:0001139 ! connected to common iliac vein relationship: RO:0002179 UBERON:0002103 ! drains hindlimb -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174692,9 +174863,9 @@ xref: Wikipedia:Internal_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein relationship: RO:0002170 UBERON:0001139 ! connected to common iliac vein relationship: RO:0002179 UBERON:0005179 ! drains pelvic region element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174731,7 +174902,7 @@ intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000996 ! vagina relationship: part_of UBERON:0000996 ! vagina relationship: RO:0002376 UBERON:0001317 {source="FMA/obol"} ! tributary of internal iliac vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174767,7 +174938,7 @@ is_a: UBERON:0001021 ! nerve relationship: overlaps UBERON:0000978 ! leg relationship: part_of UBERON:0001815 ! lumbosacral nerve plexus relationship: RO:0002134 UBERON:0001511 ! innervates skin of leg -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray1244.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray1244.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174789,7 +174960,7 @@ xref: UMLS:C0040186 {source="ncithesaurus:Tibial_Nerve"} xref: Wikipedia:Tibial_nerve is_a: UBERON:0003431 ! leg nerve relationship: RO:0002380 UBERON:0001322 {source="FMA", source="WP"} ! branching part of sciatic nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1a/Gray828.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1a/Gray828.png" xsd:anyURI [Term] id: UBERON:0001325 @@ -174852,7 +175023,7 @@ xref: Wikipedia:Pampiniform_venous_plexus is_a: UBERON:0001593 ! venous plexus relationship: RO:0001025 UBERON:0005352 ! located in spermatic cord relationship: RO:0002170 UBERON:0000442 ! connected to right testicular vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray1147.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray1147.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -174908,8 +175079,8 @@ intersection_of: part_of UBERON:0000989 ! penis relationship: adjacent_to UBERON:0001299 ! glans penis relationship: part_of UBERON:0000989 ! penis relationship: RO:0002494 UBERON:0035005 ! transformation of preputial swelling of male -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg" xsd:anyURI [Term] id: UBERON:0001333 @@ -174930,8 +175101,8 @@ is_a: UBERON:0000057 ! urethra intersection_of: UBERON:0000057 ! urethra intersection_of: part_of UBERON:0003101 ! male organism relationship: part_of UBERON:0003101 ! male organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0001334 @@ -174954,7 +175125,7 @@ is_a: UBERON:0000057 ! urethra intersection_of: UBERON:0000057 ! urethra intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0003100 ! female organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0001335 @@ -174982,8 +175153,8 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0001333 {source="FMA", source="MA"} ! male urethra relationship: RO:0001025 UBERON:0002367 {source="FMA"} ! located in prostate gland relationship: RO:0002433 UBERON:0001333 ! contributes to morphology of male urethra -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray1142.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray1142.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -175051,8 +175222,8 @@ relationship: channel_for CL:0000019 ! sperm relationship: channels_into UBERON:0003959 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! rete testis relationship: part_of UBERON:0000473 ! testis relationship: RO:0002202 UBERON:0005297 {source="Wikipedia"} ! develops from testis sex cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png" xsd:anyURI [Term] id: UBERON:0001344 @@ -175141,7 +175312,7 @@ intersection_of: UBERON:0001013 ! adipose tissue intersection_of: RO:0002473 CL:0000449 ! composed primarily of brown adipocyte relationship: capable_of GO:1990845 ! adaptive thermogenesis relationship: RO:0002473 CL:0000449 ! composed primarily of brown adipocyte -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg" xsd:anyURI [Term] id: UBERON:0001351 @@ -175162,7 +175333,7 @@ xref: Wikipedia:Lacrimal_sac is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0002392 ! nasolacrimal duct -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI [Term] id: UBERON:0001352 @@ -175227,7 +175398,7 @@ is_a: BFO:0000002 is_a: UBERON:0000475 ! organism subdivision relationship: overlaps UBERON:0006866 ! terminal part of digestive tract relationship: RO:0002254 UBERON:0000931 ! has developmental contribution from proctodeum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/507" xsd:anyURI [Term] @@ -175252,7 +175423,7 @@ intersection_of: part_of UBERON:0035551 ! deep vasculature intersection_of: RO:0002252 UBERON:0002060 ! connecting branch of femoral artery relationship: part_of UBERON:0035551 ! deep vasculature relationship: RO:0002252 UBERON:0002060 ! connecting branch of femoral artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -175274,7 +175445,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0007119 ! supplies neck of femur relationship: RO:0002178 UBERON:0007119 ! supplies neck of femur relationship: RO:0002252 UBERON:0001355 {source="FMA"} ! connecting branch of deep femoral artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -175361,7 +175532,7 @@ xref: UMLS:C0392907 {source="ncithesaurus:Long_Saphenous_Vein"} xref: Wikipedia:Great_saphenous_vein is_a: UBERON:0007318 ! saphenous vein relationship: RO:0002376 UBERON:0001361 {source="FMA/obol"} ! tributary of femoral vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Great_saphenous_vein.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Great_saphenous_vein.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -175387,7 +175558,7 @@ intersection_of: UBERON:0022351 ! parietal serous membrane intersection_of: part_of UBERON:0002358 ! peritoneum relationship: part_of UBERON:0002358 ! peritoneum relationship: RO:0002371 UBERON:0003697 ! attached to abdominal wall -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI [Term] id: UBERON:0001383 @@ -175459,7 +175630,7 @@ is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001870 {source="MA", source="Wikipedia"} ! frontal cortex relationship: RO:0002433 UBERON:0000956 ! contributes to morphology of cerebral cortex relationship: RO:0002433 UBERON:0001870 ! contributes to morphology of frontal cortex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Ba4.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Ba4.png" xsd:anyURI property_value: IAO:0000116 "TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -175490,7 +175661,7 @@ relationship: part_of UBERON:0001467 ! shoulder relationship: RO:0002170 UBERON:0001533 ! connected to subclavian artery relationship: RO:0002178 UBERON:0009472 ! supplies axilla relationship: RO:0002252 UBERON:0001394 ! connecting branch of axillary artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/88/Axillary_limits.PNG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/88/Axillary_limits.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -175510,7 +175681,7 @@ xref: UMLS:C0226422 {source="ncithesaurus:Subscapular_Artery"} xref: Wikipedia:Subscapular_artery is_a: UBERON:0001637 ! artery relationship: RO:0002170 UBERON:0001394 ! connected to axillary artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Axillary_branches.PNG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Axillary_branches.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -175756,7 +175927,7 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004452 ! carpal region disjoint_from: UBERON:0012358 ! manual digitopodium bone relationship: RO:0002202 UBERON:0006213 ! develops from carpus cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI [Term] id: UBERON:0001436 @@ -175821,7 +175992,7 @@ xref: UMLS:C1708734 {source="ncithesaurus:Long_Bone_Epiphysis"} xref: Wikipedia:Epiphysis is_a: UBERON:0005055 ! zone of long bone relationship: RO:0002433 UBERON:0002495 ! contributes to morphology of long bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI property_value: seeAlso UBERON:0006776 [Term] @@ -175874,8 +176045,8 @@ xref: UMLS:C0222661 {source="ncithesaurus:Cortical_Bone"} xref: Wikipedia:Compact_bone is_a: UBERON:0002481 ! bone tissue relationship: part_of UBERON:0002482 ! lamellar bone -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI [Term] id: UBERON:0001440 @@ -176011,7 +176182,7 @@ xref: UMLS:C1527391 {source="ncithesaurus:Chest"} xref: Wikipedia:Chest is_a: UBERON:0009569 {source="FMA-modified"} ! subdivision of trunk relationship: part_of UBERON:0000915 {source="FMA", source="MA"} ! thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg" xsd:anyURI property_value: IAO:0000116 "FMA:24216 present in FMA1, but gone in subsequent versions" xsd:string [Term] @@ -176084,7 +176255,7 @@ intersection_of: UBERON:0015013 ! fibula endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: BSPO:0001115 UBERON:0010720 ! hindlimb zeugopod skeleton relationship: RO:0002202 UBERON:0010851 ! develops from fibula cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -176121,7 +176292,7 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004454 ! tarsal region disjoint_from: UBERON:0012359 ! pedal digitopodium bone relationship: RO:0002202 UBERON:0010541 ! develops from tarsus cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI [Term] id: UBERON:0001448 @@ -176154,7 +176325,7 @@ intersection_of: part_of UBERON:0000983 ! metatarsus region relationship: part_of UBERON:0010545 ! metatarsus skeleton relationship: RO:0002170 UBERON:0001447 ! connected to tarsal bone relationship: RO:0002170 UBERON:0001449 ! connected to phalanx of pes -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI [Term] id: UBERON:0001449 @@ -176223,7 +176394,7 @@ relationship: has_part UBERON:0000165 ! mouth relationship: has_part UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! facial skeleton relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head relationship: RO:0002551 UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! has skeleton facial skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] id: UBERON:0001457 @@ -176321,7 +176492,7 @@ is_a: UBERON:0006058 ! multi-limb segment region is_a: UBERON:0008785 ! upper limb segment relationship: distally_connected_to UBERON:0002398 ! manus relationship: proximally_connected_to UBERON:0001467 ! shoulder -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg" xsd:anyURI property_value: IAO:0000116 "currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand" xsd:string [Term] @@ -176352,7 +176523,7 @@ xref: VHOG:0000340 xref: Wikipedia:Elbow is_a: UBERON:0008785 ! upper limb segment relationship: part_of UBERON:0001460 {source="EHDAA2"} ! arm -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG" xsd:anyURI [Term] id: UBERON:0001464 @@ -176385,7 +176556,7 @@ xref: Wikipedia:Hip is_a: UBERON:0000475 ! organism subdivision relationship: overlaps UBERON:0001271 {source="FMA-modified"} ! pelvic girdle region relationship: part_of UBERON:0010709 ! pelvic complex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg" xsd:anyURI [Term] id: UBERON:0001465 @@ -176412,7 +176583,7 @@ xref: SCTID:361291001 xref: VHOG:0000347 is_a: UBERON:0008784 ! lower limb segment relationship: part_of UBERON:0000978 ! leg -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -176453,7 +176624,7 @@ intersection_of: UBERON:0002544 ! digit intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0012142 {source="PHENOSCAPE:ni"} ! pedal digitopodium region relationship: part_of UBERON:5001466 ! pedal digit plus metapodial segment -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg" xsd:anyURI [Term] id: UBERON:0001467 @@ -176487,7 +176658,7 @@ relationship: has_part UBERON:0016884 ! shoulder joint relationship: overlaps UBERON:0001421 {source="FMA-modified"} ! pectoral girdle region relationship: part_of UBERON:0010708 ! pectoral complex relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG" xsd:anyURI [Term] id: UBERON:0001468 @@ -176537,7 +176708,7 @@ intersection_of: RO:0002176 UBERON:0000975 ! connects sternum intersection_of: RO:0002176 UBERON:0001105 ! connects clavicle bone relationship: RO:0002176 UBERON:0000975 ! connects sternum relationship: RO:0002176 UBERON:0001105 ! connects clavicle bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png" xsd:anyURI [Term] id: UBERON:0001470 @@ -176571,7 +176742,7 @@ relationship: adjacent_to UBERON:0006657 ! glenoid fossa relationship: part_of UBERON:0004753 ! scapulocoracoid relationship: RO:0002176 UBERON:0000976 ! connects humerus relationship: RO:0002176 UBERON:0006849 ! connects scapula -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png" xsd:anyURI property_value: IAO:0000116 "note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship" xsd:string [Term] @@ -176611,7 +176782,7 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0001593 ! venous plexus intersection_of: part_of UBERON:0000996 ! vagina relationship: part_of UBERON:0000996 ! vagina -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI [Term] id: UBERON:0001473 @@ -176647,7 +176818,7 @@ disjoint_from: UBERON:0001981 ! blood vessel relationship: has_part UBERON:0002391 ! lymph relationship: part_of UBERON:0004536 ! lymph vasculature relationship: RO:0002433 UBERON:0002405 ! contributes to morphology of immune system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -176745,7 +176916,7 @@ relationship: RO:0002372 UBERON:0002497 ! has muscle origin acromion relationship: RO:0002372 UBERON:0006849 ! has muscle origin scapula relationship: RO:0002373 UBERON:0002498 ! has muscle insertion deltopectoral crest relationship: RO:0002568 UBERON:0001112 {source="dbpedia"} ! has muscle antagonist latissimus dorsi muscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -176773,7 +176944,7 @@ is_a: UBERON:0013630 {source="UBERON:cjm"} ! short bone is_a: UBERON:0013631 ! sesamoid element intersection_of: UBERON:0013631 ! sesamoid element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png" xsd:anyURI [Term] id: UBERON:0001480 @@ -176858,8 +177029,8 @@ intersection_of: has_part UBERON:0007616 ! layer of synovial tissue intersection_of: RO:0002221 UBERON:0002217 ! surrounds synovial joint relationship: has_part UBERON:0007616 ! layer of synovial tissue relationship: RO:0002221 UBERON:0002217 ! surrounds synovial joint -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png" xsd:anyURI [Term] id: UBERON:0001485 @@ -176896,7 +177067,7 @@ relationship: RO:0002176 UBERON:0000979 ! connects tibia relationship: RO:0002176 UBERON:0000981 ! connects femur relationship: RO:0002176 UBERON:0002446 ! connects patella relationship: RO:0002202 UBERON:0006256 ! develops from knee joint primordium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -176962,7 +177133,7 @@ relationship: RO:0002176 UBERON:0000979 {gci_relation="part_of", gci_filler="NCB relationship: RO:0002176 UBERON:0001445 ! connects skeleton of pes relationship: RO:0002176 UBERON:0001446 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! connects fibula relationship: RO:0002176 UBERON:0010720 ! connects hindlimb zeugopod skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI [Term] id: UBERON:0001489 @@ -177047,7 +177218,7 @@ intersection_of: RO:0002176 UBERON:0010703 ! connects forelimb zeugopod skeleton relationship: part_of UBERON:0004452 ! carpal region relationship: RO:0002176 UBERON:0009880 ! connects carpal skeleton relationship: RO:0002176 UBERON:0010703 ! connects forelimb zeugopod skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI [Term] id: UBERON:0001493 @@ -177070,8 +177241,8 @@ xref: Wikipedia:Axillary_nerve is_a: UBERON:0003433 ! arm nerve relationship: part_of UBERON:0001814 {source="MA"} ! brachial nerve plexus relationship: RO:0002134 UBERON:0009472 ! innervates axilla -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177106,7 +177277,7 @@ is_a: UBERON:0003830 ! thoracic segment muscle is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0008196 {source="FMA"} ! muscle of pectoral girdle relationship: RO:0002202 UBERON:0010984 ! develops from pectoral pre-muscle mass -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177136,9 +177307,9 @@ relationship: RO:0002202 UBERON:0005338 {source="EHDAA2"} ! develops from outflo relationship: RO:0002254 UBERON:0002061 ! has developmental contribution from truncus arteriosus relationship: RO:0002254 UBERON:0005432 ! has developmental contribution from aortic sac relationship: RO:0002433 UBERON:0001515 ! contributes to morphology of thoracic aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177258,9 +177429,9 @@ relationship: RO:0002202 UBERON:0003121 ! develops from pharyngeal arch artery 4 relationship: RO:0002254 UBERON:0005432 ! has developmental contribution from aortic sac relationship: RO:0002254 UBERON:0005613 ! has developmental contribution from left dorsal aorta relationship: RO:0002433 UBERON:0001515 ! contributes to morphology of thoracic aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177364,9 +177535,9 @@ relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta relationship: RO:0002202 UBERON:0005805 {source="Wikipedia"} ! develops from dorsal aorta relationship: RO:0002254 UBERON:0005613 ! has developmental contribution from left dorsal aorta relationship: RO:0002254 UBERON:0005622 ! has developmental contribution from right dorsal aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177398,7 +177569,7 @@ intersection_of: UBERON:0005800 ! section of aorta intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: RO:0002433 UBERON:0000947 ! contributes to morphology of aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png" xsd:anyURI [Term] id: UBERON:0001516 @@ -177432,7 +177603,7 @@ relationship: overlaps UBERON:0000916 ! abdomen relationship: part_of UBERON:0001514 {source="FMA"} ! descending aorta relationship: RO:0002170 UBERON:0002345 ! connected to descending thoracic aorta relationship: RO:0002433 UBERON:0001514 ! contributes to morphology of descending aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI property_value: IAO:0000116 "Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -177531,9 +177702,9 @@ is_a: UBERON:0004573 ! systemic artery relationship: channels_from UBERON:0001508 ! arch of aorta relationship: part_of UBERON:0007204 ! brachiocephalic vasculature relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177566,7 +177737,7 @@ is_a: UBERON:0004573 {source="FMA"} ! systemic artery relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta relationship: RO:0002202 UBERON:0004363 {source="Wikipedia"} ! develops from pharyngeal arch artery relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI property_value: IAO:0000116 "we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -177590,7 +177761,7 @@ xref: Wikipedia:Right_common_carotid_artery is_a: UBERON:0001530 {source="FMA"} ! common carotid artery plus branches relationship: RO:0002170 UBERON:0001529 ! connected to brachiocephalic artery relationship: RO:0002380 UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! branching part of brachiocephalic artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177633,7 +177804,7 @@ relationship: RO:0002178 UBERON:0000955 ! supplies brain relationship: RO:0002178 UBERON:0000970 ! supplies eye relationship: RO:0002202 UBERON:2001053 {source="cjm"} ! develops from future internal carotid artery relationship: RO:0002380 UBERON:0001530 {source="FMA"} ! branching part of common carotid artery plus branches -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177673,7 +177844,7 @@ relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta relationship: RO:0002178 UBERON:0004710 ! supplies pectoral appendage relationship: RO:0002202 UBERON:0002457 {source="EHDAA2"} ! develops from intersomitic artery relationship: RO:0002202 UBERON:0005622 {source="EHDAA2"} ! develops from right dorsal aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI property_value: IAO:0000116 "Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -177701,7 +177872,7 @@ intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: RO:0002170 UBERON:0001529 ! connected to brachiocephalic artery relationship: RO:0002380 UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! branching part of brachiocephalic artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177722,9 +177893,9 @@ xref: SCTID:362043008 xref: UMLS:C0226087 {source="ncithesaurus:Left_Common_Carotid_Artery"} xref: Wikipedia:Left_common_carotid_artery is_a: UBERON:0001530 {source="FMA"} ! common carotid artery plus branches -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177748,7 +177919,7 @@ xref: Wikipedia:Popliteal_vein is_a: UBERON:0001638 ! vein relationship: overlaps UBERON:0001465 ! knee relationship: RO:0002376 UBERON:0001361 {source="FMA/obol"} ! tributary of femoral vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray609.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray609.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177770,7 +177941,7 @@ xref: Wikipedia:Anterior_tibial_vein is_a: UBERON:0010370 {source="MA"} ! tibial vein relationship: RO:0002376 UBERON:0001361 {source="FMA/obol"} ! tributary of femoral vein relationship: RO:0002376 UBERON:0001544 {source="FMA/obol"} ! tributary of popliteal vein -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4e/Gray440_color.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/4e/Gray440_color.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177794,7 +177965,7 @@ xref: UMLS:C0226827 {source="ncithesaurus:Short_Saphenous_Vein"} xref: Wikipedia:Small_saphenous_vein is_a: UBERON:0007318 ! saphenous vein relationship: RO:0002376 UBERON:0001544 {source="FMA"} ! tributary of popliteal vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/62/Gray582.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/62/Gray582.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177853,7 +178024,7 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney relationship: RO:0002252 UBERON:0009885 ! connecting branch of interlobar artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177899,7 +178070,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -177956,8 +178127,8 @@ xref: VHOG:0000406 xref: Wikipedia:Upper_respiratory_tract is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: has_part UBERON:0000004 ! nose -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -177978,8 +178149,8 @@ xref: VHOG:0000382 xref: Wikipedia:Lower_respiratory_tract is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: has_part UBERON:0000170 ! pair of lungs -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178050,7 +178221,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: RO:0002202 UBERON:0010059 {source="EHDAA2"} ! develops from hypoglossal cord relationship: RO:0002372 UBERON:0006606 ! has muscle origin mandibular symphysis relationship: RO:0002373 UBERON:0009471 {source="Wikipedia"} ! has muscle insertion dorsum of tongue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178080,7 +178251,7 @@ relationship: RO:0002371 UBERON:0001685 ! attached to hyoid bone relationship: RO:0002371 UBERON:0001723 ! attached to tongue relationship: RO:0002372 UBERON:0001685 ! has muscle origin hyoid bone relationship: RO:0002373 UBERON:0001723 ! has muscle insertion tongue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178171,7 +178342,7 @@ intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: RO:0002005 UBERON:0001647 ! innervated_by facial nerve relationship: RO:0002005 UBERON:0001647 ! innervated_by facial nerve relationship: RO:0002202 UBERON:0003066 {source="FEED", source="Wikipedia"} ! develops from pharyngeal arch 2 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI [Term] id: UBERON:0001579 @@ -178228,7 +178399,7 @@ intersection_of: RO:0002134 UBERON:0001997 ! innervates olfactory epithelium relationship: extends_fibers_into UBERON:0002264 ! olfactory bulb relationship: RO:0002134 UBERON:0001997 {source="ISBN:0471888893"} ! innervates olfactory epithelium relationship: RO:0002202 UBERON:0003050 {source="ISBN:0471888893"} ! develops from olfactory placode -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178253,9 +178424,9 @@ intersection_of: UBERON:0001533 ! subclavian artery intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: channels_from UBERON:0001508 ! arch of aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178291,7 +178462,7 @@ intersection_of: UBERON:0004087 ! vena cava intersection_of: RO:0002179 UBERON:0000153 ! drains anterior region of body relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium relationship: RO:0002179 UBERON:0000153 ! drains anterior region of body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178321,7 +178492,7 @@ is_a: UBERON:0004711 ! jugular vein relationship: RO:0002170 UBERON:0003711 ! connected to brachiocephalic vein relationship: RO:0002179 UBERON:0000955 ! drains brain relationship: RO:0002179 UBERON:0001456 ! drains face -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178349,7 +178520,7 @@ xref: Wikipedia:Subclavian_vein is_a: UBERON:0001638 ! vein relationship: RO:0002170 UBERON:0003711 ! connected to brachiocephalic vein relationship: RO:0002179 UBERON:0004710 ! drains pectoral appendage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178415,7 +178586,7 @@ is_a: UBERON:0005629 ! vascular plexus intersection_of: UBERON:0005629 ! vascular plexus intersection_of: RO:0002473 UBERON:0001638 ! composed primarily of vein relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI [Term] id: UBERON:0001605 @@ -178441,7 +178612,7 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178501,7 +178672,7 @@ relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops fr relationship: RO:0002372 UBERON:0001769 ! has muscle origin iris relationship: RO:0002373 UBERON:0001769 ! has muscle insertion iris relationship: RO:0002568 UBERON:0001608 {source="dbpedia"} ! has muscle antagonist dilatator pupillae -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI [Term] id: UBERON:0001608 @@ -178541,7 +178712,7 @@ relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops fr relationship: RO:0002372 UBERON:0001769 ! has muscle origin iris relationship: RO:0002373 UBERON:0001769 ! has muscle insertion iris relationship: RO:0002568 UBERON:0001607 {source="dbpedia"} ! has muscle antagonist sphincter pupillae -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178567,7 +178738,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001723 ! supplies tongue relationship: BSPO:0000126 UBERON:0001723 {source="FMA-abduced-lr"} ! tongue relationship: RO:0002178 UBERON:0001723 ! supplies tongue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178591,7 +178762,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001456 ! supplies face intersection_of: RO:0002252 UBERON:0001070 ! connecting branch of external carotid artery relationship: RO:0002178 UBERON:0001456 ! supplies face -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178616,7 +178787,7 @@ intersection_of: RO:0002178 UBERON:0002377 ! supplies muscle of neck intersection_of: RO:0002252 UBERON:0001070 ! connecting branch of external carotid artery relationship: RO:0002178 UBERON:0000403 ! supplies scalp relationship: RO:0002178 UBERON:0002377 ! supplies muscle of neck -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178644,7 +178815,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002207 UBERON:0003118 ! directly develops from pharyngeal arch artery 1 relationship: RO:0002170 UBERON:0001070 ! connected to external carotid artery relationship: RO:0002207 UBERON:0003118 ! directly develops from pharyngeal arch artery 1 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178671,9 +178842,9 @@ xref: Wikipedia:Ophthalmic_artery xref: XAO:0000368 is_a: UBERON:0001637 ! artery relationship: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178703,7 +178874,7 @@ xref: ZFA:0005812 is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0004573 ! systemic artery relationship: RO:0002178 UBERON:0002349 ! supplies myocardium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI [Term] id: UBERON:0001622 @@ -178725,7 +178896,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001817 ! supplies lacrimal gland relationship: RO:0002178 UBERON:0001817 ! supplies lacrimal gland relationship: RO:0002252 UBERON:0001619 {source="FMA"} ! connecting branch of ophthalmic artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178762,7 +178933,7 @@ intersection_of: RO:0002252 UBERON:0001532 ! connecting branch of internal carot relationship: BSPO:0000126 UBERON:0003709 {source="FMA-abduced-lr"} ! circle of Willis relationship: part_of UBERON:0003709 ! circle of Willis relationship: RO:0002252 UBERON:0001532 {source="FMA", source="ZFA"} ! connecting branch of internal carotid artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178877,7 +179048,7 @@ intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string [Term] @@ -178909,9 +179080,9 @@ relationship: channels_into UBERON:0002107 ! liver relationship: overlaps UBERON:0002107 ! liver relationship: part_of UBERON:0010194 ! hepatic portal system relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178949,7 +179120,7 @@ relationship: indirectly_supplies UBERON:0000945 {source="ISBN:0073040584"} ! st relationship: indirectly_supplies UBERON:0002106 {source="ISBN:0073040584"} ! spleen relationship: indirectly_supplies UBERON:0002107 {source="ISBN:0073040584"} ! liver relationship: RO:0002202 UBERON:0006002 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia"} ! develops from vitelline artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -178988,7 +179159,6 @@ xref: EHDAA:3738 xref: EMAPA:17576 xref: FMA:50866 xref: GAID:726 -xref: HBA:9322 xref: MA:0001100 xref: MBA:901 xref: MESH:D014276 @@ -179013,7 +179183,7 @@ relationship: RO:0002134 UBERON:0000165 ! innervates mouth relationship: RO:0002134 UBERON:0011648 ! innervates jaw muscle relationship: RO:0002134 UBERON:1000021 ! innervates skin of face relationship: RO:0002254 UBERON:0005239 {source="Wikipedia"} ! has developmental contribution from basal plate metencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179077,7 +179247,7 @@ relationship: part_of UBERON:0001033 {source="ZFA"} ! gustatory system relationship: RO:0002134 UBERON:0001577 ! innervates facial muscle relationship: RO:0002254 UBERON:0003066 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 2 relationship: RO:0002254 UBERON:0005239 {source="Wikipedia"} ! has developmental contribution from basal plate metencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179143,7 +179313,7 @@ relationship: extends_fibers_into UBERON:0001720 ! cochlear nucleus relationship: part_of UBERON:0002105 ! vestibulo-auditory system relationship: RO:0002134 UBERON:0001844 ! innervates cochlea relationship: RO:0002202 UBERON:0003069 {source="ISBN:0471888893"} ! develops from otic placode -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179177,7 +179347,6 @@ xref: EHDAA:3733 xref: EMAPA:17268 xref: FMA:50870 xref: GAID:827 -xref: HBA:9334 xref: MA:0001093 xref: MBA:808 xref: MESH:D005930 @@ -179197,7 +179366,7 @@ relationship: part_of UBERON:0001033 ! gustatory system relationship: RO:0002134 UBERON:0001727 ! innervates taste bud relationship: RO:0002134 UBERON:0006562 ! innervates pharynx relationship: RO:0002254 UBERON:0005239 ! has developmental contribution from basal plate metencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179232,7 +179401,6 @@ xref: EHDAA:2859 xref: EMAPA:17269 xref: FMA:50871 xref: GAID:828 -xref: HBA:9343 xref: MA:0001094 xref: MBA:813 xref: MESH:D007002 @@ -179251,7 +179419,7 @@ relationship: extends_fibers_into UBERON:0002871 ! hypoglossal nucleus relationship: RO:0002134 UBERON:0001571 ! innervates genioglossus muscle relationship: RO:0002134 UBERON:0001572 ! innervates hyoglossus muscle relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179277,10 +179445,10 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0002167 ! supplies right lung relationship: RO:0002170 UBERON:0002333 ! connected to pulmonary trunk relationship: RO:0002178 UBERON:0002167 ! supplies right lung -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: IAO:0000116 "TODO - add class 'pulmonary artery tree organ'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -179307,10 +179475,10 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0002168 ! supplies left lung relationship: RO:0002170 UBERON:0002333 ! connected to pulmonary trunk relationship: RO:0002178 UBERON:0002168 ! supplies left lung -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: IAO:0000116 "TODO - add class 'pulmonary artery tree organ'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -179337,7 +179505,7 @@ is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001456 ! face relationship: RO:0002376 UBERON:0001586 {source="FMA"} ! tributary of internal jugular vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179364,7 +179532,7 @@ intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0001893 ! drains telencephalon relationship: part_of UBERON:0001893 ! telencephalon relationship: RO:0002179 UBERON:0001893 ! drains telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png" xsd:anyURI [Term] id: UBERON:0001668 @@ -179441,7 +179609,7 @@ intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: RO:0002495 UBERON:0006304 {source="Bgee:AN"} ! immediate transformation of future trigeminal ganglion -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png" xsd:anyURI property_value: IAO:0000116 "consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)" xsd:string [Term] @@ -179474,7 +179642,7 @@ relationship: RO:0002170 UBERON:0001092 {gci_relation="part_of", gci_filler="NCB relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone relationship: RO:0002202 UBERON:0003089 {source="PMID:11523816"} ! develops from sclerotome relationship: RO:0002221 UBERON:0003687 ! surrounds foramen magnum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179516,7 +179684,7 @@ relationship: RO:0002170 UBERON:0001676 {gci_relation="part_of", gci_filler="NCB relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone relationship: RO:0002170 UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vomer relationship: RO:0002202 UBERON:0009193 {source="cjm"} ! develops from sphenoid cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179543,7 +179711,7 @@ is_a: UBERON:0008193 {source="FMA"} ! pneumatized bone relationship: overlaps UBERON:0002241 ! chondrocranium relationship: overlaps UBERON:0003113 ! dermatocranium relationship: overlaps UBERON:0008895 ! splanchnocranium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179578,7 +179746,7 @@ relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCB relationship: RO:0002170 UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vomer relationship: RO:0002202 UBERON:0006227 ! develops from ethmoid bone primordium relationship: RO:0002433 UBERON:0011156 ! contributes to morphology of facial skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179609,7 +179777,7 @@ is_a: UBERON:0008001 {source="FMA"} ! irregular bone relationship: part_of UBERON:0010272 ! hyoid apparatus relationship: RO:0002254 UBERON:0003066 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 2 relationship: RO:0002254 UBERON:0003114 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 3 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -179647,7 +179815,7 @@ is_a: UBERON:0003457 ! head bone is_a: UBERON:0035130 ! auditory ossicle endochondral element intersection_of: UBERON:0035130 ! auditory ossicle endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg" xsd:anyURI property_value: IAO:0000116 "This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5." xsd:string [Term] @@ -179689,7 +179857,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0002105 ! vestibulo-auditory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg" xsd:anyURI [Term] id: UBERON:0001691 @@ -179731,7 +179899,7 @@ relationship: part_of UBERON:0001690 ! ear relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head relationship: RO:0002433 UBERON:0001690 ! contributes to morphology of ear -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:9709 {source="Wikipedia"} [Term] @@ -179761,7 +179929,7 @@ xref: Wikipedia:Petrous_part_of_the_temporal_bone is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0001678 ! temporal bone relationship: part_of UBERON:0002517 {source="FMA"} ! basicranium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray137.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray137.png" xsd:anyURI [Term] id: UBERON:0001697 @@ -179801,6 +179969,7 @@ name: geniculate ganglion namespace: uberon def: "The group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve)." [ISBN:0-683-40008-8, MP:0001082] subset: efo_slim +subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -179842,8 +180011,9 @@ relationship: extends_fibers_into UBERON:0001647 ! facial nerve relationship: RO:0002202 UBERON:0009124 {source="EHDAA2:0004623", source="ZFA"} ! develops from geniculate placode relationship: RO:0002202 UBERON:0010258 {source="EHDAA2:0004623"} ! develops from mesenchyme from rhombencephalic neural crest relationship: RO:0002202 UBERON:0012175 {source="EHDAA2:0000491"} ! develops from acoustico-facial VII-VIII ganglion complex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI property_value: IAO:0000116 "resolve facial VII vs geniculate (see EHDAA2)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001701 @@ -179976,7 +180146,7 @@ is_a: BFO:0000002 is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0015788 {source="cjm"} ! olfactory apparatus chamber relationship: RO:0002202 UBERON:0005870 ! develops from olfactory pit -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI property_value: IAO:0000116 "define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong." xsd:string [Term] @@ -180054,7 +180224,7 @@ disjoint_from: UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0004089 ! midface relationship: part_of UBERON:0011595 ! jaw region relationship: RO:0002551 UBERON:0003277 ! has skeleton skeleton of upper jaw -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png" xsd:anyURI [Term] id: UBERON:0001710 @@ -180086,7 +180256,7 @@ intersection_of: RO:0002551 UBERON:0003278 ! has skeleton skeleton of lower jaw relationship: part_of UBERON:0011595 ! jaw region relationship: RO:0002202 UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! develops from mandibular prominence relationship: RO:0002551 UBERON:0003278 ! has skeleton skeleton of lower jaw -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI [Term] id: UBERON:0001711 @@ -180120,7 +180290,7 @@ relationship: capable_of GO:0060082 ! eye blink reflex relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye relationship: protects UBERON:0010409 ! ocular surface region relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI [Term] id: UBERON:0001714 @@ -180197,7 +180367,7 @@ intersection_of: part_of UBERON:0002610 ! cochlear nuclear complex relationship: extends_fibers_into UBERON:0004727 ! cochlear nerve relationship: part_of UBERON:0002610 ! cochlear nuclear complex relationship: RO:0002433 UBERON:0002298 ! contributes to morphology of brainstem -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI [Term] id: UBERON:0001723 @@ -180244,7 +180414,7 @@ relationship: RO:0002254 UBERON:0006756 {source="Wikipedia"} ! has developmental relationship: RO:0002254 UBERON:0006757 {source="Wikipedia"} ! has developmental contribution from lateral lingual swelling relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system relationship: RO:0002495 UBERON:0010056 ! immediate transformation of future tongue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg" xsd:anyURI property_value: IAO:0000116 "in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence." xsd:string [Term] @@ -180318,7 +180488,7 @@ relationship: has_part CL:0000209 {source="FMA"} ! taste receptor cell relationship: part_of UBERON:0002926 {source="NIF"} ! gustatory epithelium relationship: RO:0002202 UBERON:0007690 {source="http://dev.biologists.org/content/128/22/4573.full"} ! develops from early pharyngeal endoderm relationship: RO:0002433 UBERON:0001033 ! contributes to morphology of gustatory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png" xsd:anyURI [Term] id: UBERON:0001728 @@ -180352,7 +180522,7 @@ is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001557 ! upper respiratory tract relationship: RO:0002433 UBERON:0001042 ! contributes to morphology of chordate pharynx -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg" xsd:anyURI [Term] id: UBERON:0001731 @@ -180433,9 +180603,9 @@ is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: RO:0002005 UBERON:0003716 ! innervated_by recurrent laryngeal nerve relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI [Term] id: UBERON:0001739 @@ -180464,8 +180634,8 @@ intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0001737 ! larynx relationship: part_of UBERON:0010212 ! laryngeal apparatus relationship: RO:0002202 UBERON:0010213 ! develops from laryngeal pre-cartilage condensation -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI [Term] id: UBERON:0001743 @@ -180529,7 +180699,7 @@ intersection_of: has_part UBERON:0010754 ! germinal center relationship: BFO:0000067 GO:0042100 ! contains process B cell proliferation relationship: has_part UBERON:0010754 ! germinal center relationship: RO:0002202 UBERON:0010422 ! develops from primary nodular lymphoid tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Keimzentrum.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Keimzentrum.jpg" xsd:anyURI [Term] id: UBERON:0001746 @@ -180643,7 +180813,7 @@ relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI property_value: IAO:0000116 "TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal" xsd:string [Term] @@ -180707,7 +180877,7 @@ is_a: UBERON:4000013 ! mineralized skeletal tissue relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0011588 {source="VSAO"} ! develops from pre-enamel relationship: RO:0002473 CHEBI:52255 ! composed primarily of -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg" xsd:anyURI property_value: IAO:0000116 "current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)" xsd:string property_value: RO:0002161 NCBITaxon:9359 {source="PMID:19730686"} property_value: RO:0002161 NCBITaxon:9816 {source="PMID:19730686"} @@ -180737,7 +180907,7 @@ xref: Wikipedia:Cementum xref: XAO:0004196 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: RO:0002254 UBERON:0008969 {source="PMID:19767574", source="Wikipedia"} ! has developmental contribution from dental follicle -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI [Term] id: UBERON:0001754 @@ -180769,7 +180939,7 @@ is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: has_part CL:0000060 ! odontoblast relationship: part_of UBERON:0001091 ! calcareous tooth relationship: RO:0002202 UBERON:0001763 {source="ZFA"} ! develops from odontogenic papilla -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI [Term] id: UBERON:0001756 @@ -180859,7 +181029,7 @@ is_a: UBERON:0000479 {source="cjm"} ! tissue relationship: adjacent_to UBERON:0001091 ! calcareous tooth relationship: has_part CL:0002166 {source="FMA"} ! epithelial cell of Malassez relationship: part_of UBERON:0003672 {source="cjm"} ! dentition -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI [Term] id: UBERON:0001759 @@ -180895,7 +181065,6 @@ xref: EMAPA:37797 {source="MA:th"} xref: FMA:5731 xref: GAID:721 xref: galen:VagusNerve -xref: HBA:9337 xref: MA:0001106 xref: MBA:917 xref: MESH:D014630 @@ -180917,7 +181086,7 @@ relationship: extends_fibers_into UBERON:0002075 ! viscus relationship: extends_fibers_into UBERON:0011775 ! vagus nerve nucleus relationship: part_of UBERON:0001033 ! gustatory system relationship: RO:0002254 UBERON:0005239 ! has developmental contribution from basal plate metencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -180956,7 +181125,7 @@ relationship: part_of UBERON:0008281 ! tooth bud relationship: RO:0001025 UBERON:0001828 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA-implied"} ! located in gingiva relationship: RO:0002202 UBERON:0003856 {source="ZFA"} ! develops from uncondensed odontogenic mesenchyme relationship: RO:0002473 CL:0007003 ! composed primarily of preodontoblast -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png" xsd:anyURI [Term] id: UBERON:0001765 @@ -180990,7 +181159,7 @@ intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0001911 ! mammary gland relationship: channel_for UBERON:0001913 ! milk relationship: channels_into UBERON:0002030 ! nipple -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI [Term] id: UBERON:0001766 @@ -181021,7 +181190,7 @@ xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001768 @@ -181055,7 +181224,7 @@ relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI property_value: IAO:0000116 "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} @@ -181166,7 +181335,7 @@ intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -181202,7 +181371,7 @@ relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball relationship: RO:0000086 PATO:0000963 ! has quality opaque relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -181270,7 +181439,7 @@ relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -181314,7 +181483,7 @@ relationship: overlaps UBERON:0001802 {source="Wikipedia"} ! posterior segment o relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: IAO:0000116 "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -181353,7 +181522,7 @@ relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea relationship: part_of UBERON:0000964 ! cornea relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI [Term] id: UBERON:0001778 @@ -181404,7 +181573,7 @@ intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0001769 ! iris relationship: RO:0002433 UBERON:0001769 ! contributes to morphology of iris -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI [Term] id: UBERON:0001780 @@ -181445,7 +181614,7 @@ is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0002240 ! spinal cord relationship: extends_fibers_into UBERON:0002240 ! spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -181524,7 +181693,7 @@ relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor la relationship: adjacent_to UBERON:0003902 ! retinal neural layer relationship: has_part GO:0048770 ! pigment granule relationship: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -181547,7 +181716,6 @@ xref: EHDAA2:0000323 xref: EMAPA:17264 xref: FMA:5865 xref: GAID:802 -xref: HBA:9299 xref: MA:0000215 xref: MBA:967 xref: MESH:D003391 @@ -181570,8 +181738,8 @@ intersection_of: BSPO:0000096 UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0000955 ! brain relationship: BSPO:0000096 UBERON:0001780 ! spinal nerve relationship: RO:0002254 UBERON:0003099 ! has developmental contribution from cranial neural crest -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg" xsd:anyURI property_value: IAO:0000116 "classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -181607,7 +181775,7 @@ relationship: has_part CHEBI:28838 relationship: has_part CL:0000573 ! retinal cone cell relationship: part_of UBERON:0000053 ! macula lutea relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001787 @@ -181637,7 +181805,7 @@ is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001788 ! outer limiting layer of retina relationship: has_part CL:0000287 {source="ZFA"} ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001788 @@ -181828,7 +181996,7 @@ relationship: adjacent_to UBERON:0001793 ! nerve fiber layer of retina relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer relationship: RO:0002473 CL:0000740 ! composed primarily of retinal ganglion cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -181945,7 +182113,7 @@ relationship: overlaps CL:0000740 ! retinal ganglion cell relationship: overlaps CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001796 @@ -181976,7 +182144,7 @@ is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid relationship: part_of UBERON:0001766 ! anterior chamber of eyeball relationship: RO:0002433 UBERON:0001766 ! contributes to morphology of anterior chamber of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001797 @@ -182011,7 +182179,7 @@ is_a: UBERON:0006312 ! ocular refractive media relationship: part_of UBERON:0001798 ! vitreous body relationship: RO:0000086 PATO:0000964 ! has quality transparent relationship: RO:0001025 UBERON:0005606 ! located in hyaloid cavity -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001798 @@ -182034,7 +182202,7 @@ is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball relationship: RO:0002254 UBERON:0002346 ! has developmental contribution from neurectoderm relationship: RO:0002473 UBERON:0001797 ! composed primarily of vitreous humor -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: IAO:0000116 "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string [Term] @@ -182114,7 +182282,7 @@ disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball relationship: BSPO:0000123 UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI [Term] id: UBERON:0001802 @@ -182143,7 +182311,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: BSPO:0000122 UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001803 @@ -182208,7 +182376,7 @@ relationship: has_part CHEBI:35722 relationship: has_part GO:0005587 ! collagen type IV trimer relationship: RO:0000086 PATO:0000964 ! has quality transparent relationship: RO:0002202 UBERON:0005614 {source="EHDAA2"} ! develops from lens anterior epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI [Term] id: UBERON:0001805 @@ -182236,7 +182404,7 @@ intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0002410 ! autonomic nervous system relationship: extends_fibers_into UBERON:0034728 ! autonomic nerve relationship: part_of UBERON:0002410 ! autonomic nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -182271,7 +182439,7 @@ relationship: extends_fibers_into UBERON:0034729 ! sympathetic nerve relationship: part_of UBERON:0000013 ! sympathetic nervous system relationship: RO:0002202 UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ISBN:0073040584"} ! develops from trunk neural crest relationship: RO:0002433 UBERON:0000013 ! contributes to morphology of sympathetic nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI [Term] id: UBERON:0001807 @@ -182304,7 +182472,7 @@ is_a: UBERON:0007134 {source="ZFA"} ! trunk ganglion intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0000407 ! sympathetic trunk relationship: part_of UBERON:0000407 ! sympathetic trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -182333,7 +182501,7 @@ intersection_of: part_of UBERON:0000011 ! parasympathetic nervous system relationship: extends_fibers_into UBERON:0004293 ! parasympathetic nerve relationship: part_of UBERON:0000011 ! parasympathetic nervous system relationship: RO:0002433 UBERON:0000011 ! contributes to morphology of parasympathetic nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -182414,7 +182582,7 @@ relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -182422,6 +182590,7 @@ id: UBERON:0001813 name: spinal nerve plexus namespace: uberon def: "An intermingling of fiber fascicles from adjacent spinal nerves to form a network." [http://www.medilexicon.com/medicaldictionary.php?t=70024] +subset: human_reference_atlas synonym: "plexus nervorum spinalium" EXACT OMO:0003011 [FMA:5903, FMA:TA] synonym: "plexus of spinal nerves" EXACT [FMA:5903] synonym: "somatic nerve plexus" EXACT [FMA:5903] @@ -182438,6 +182607,7 @@ is_a: UBERON:0001810 ! nerve plexus intersection_of: UBERON:0001810 ! nerve plexus intersection_of: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0001780 ! spinal nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001814 @@ -182463,8 +182633,8 @@ xref: Wikipedia:Brachial_plexus is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0001813 ! spinal nerve plexus relationship: RO:0002134 UBERON:0002102 ! innervates forelimb -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg" xsd:anyURI property_value: IAO:0000116 "check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -182493,7 +182663,7 @@ xref: Wikipedia:Lumbosacral_plexus is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0001813 ! spinal nerve plexus relationship: RO:0002134 UBERON:0002103 ! innervates hindlimb -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Gray822.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Gray822.png" xsd:anyURI [Term] id: UBERON:0001816 @@ -182551,7 +182721,7 @@ intersection_of: part_of UBERON:0001750 ! lacrimal apparatus relationship: part_of UBERON:0001750 ! lacrimal apparatus relationship: RO:0002202 UBERON:0022284 ! develops from lacrimal gland bud relationship: RO:0002433 UBERON:0001750 ! contributes to morphology of lacrimal apparatus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:8570 {source="PMID:7559104"} [Term] @@ -182586,7 +182756,7 @@ relationship: produces UBERON:0001089 ! sweat relationship: RO:0000086 PATO:0002299 ! has quality tubular relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia relationship: RO:0002202 UBERON:0005089 ! develops from sweat gland placode -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI property_value: IAO:0000116 "TODO - check if all sweat glands are epidermal - see EMAPA:29743" xsd:string [Term] @@ -182621,7 +182791,7 @@ relationship: part_of UBERON:0011932 ! pilosebaceous unit relationship: produces UBERON:0001866 ! sebum relationship: RO:0002160 NCBITaxon:40674 {source="VHOG"} ! only in taxon Mammalia relationship: RO:0002202 UBERON:0005088 ! develops from sebaceous gland placode -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -182648,7 +182818,7 @@ intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0000004 ! nose relationship: part_of UBERON:0000004 ! nose relationship: RO:0001015 UBERON:0000402 ! location of nasal vestibule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png" xsd:anyURI [Term] id: UBERON:0001824 @@ -182770,7 +182940,7 @@ relationship: adjacent_to UBERON:0008266 ! periodontal ligament relationship: part_of UBERON:0003729 {source="Carranza"} ! mouth mucosa relationship: part_of UBERON:0011595 ! jaw region relationship: RO:0002150 UBERON:0003729 {source="ISBN:0013002015"} ! continuous with mouth mucosa -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI property_value: IAO:0000116 "FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton." xsd:string [Term] @@ -182802,8 +182972,8 @@ is_a: UBERON:0003102 {source="ZFA"} ! surface structure relationship: part_of UBERON:0000165 {source="BTO", source="FMA-implicit", source="VHOG", source="ZFA"} ! mouth relationship: RO:0002221 UBERON:0000166 {source="cjm"} ! surrounds oral opening relationship: RO:0002433 UBERON:0000165 ! contributes to morphology of mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI property_value: RO:0002161 NCBITaxon:8782 [Term] @@ -182831,7 +183001,7 @@ intersection_of: UBERON:0001833 ! lip intersection_of: part_of UBERON:0001709 ! upper jaw region relationship: part_of UBERON:0001709 ! upper jaw region relationship: RO:0002495 UBERON:0011592 ! immediate transformation of future upper lip -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI [Term] id: UBERON:0001835 @@ -182859,7 +183029,7 @@ intersection_of: UBERON:0001833 ! lip intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0001710 ! lower jaw region relationship: RO:0002202 UBERON:0011596 ! develops from future lower lip -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI [Term] id: UBERON:0001836 @@ -182945,7 +183115,7 @@ is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001694 {source="FMA", source="MA"} ! petrous part of temporal bone relationship: part_of UBERON:0001846 {source="FMA"} ! internal ear relationship: part_of UBERON:0004681 ! vestibular system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png" xsd:anyURI [Term] id: UBERON:0001840 @@ -182981,7 +183151,7 @@ is_a: UBERON:0000025 {source="GO"} ! tube is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001849 {source="OG"} ! membranous labyrinth relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png" xsd:anyURI [Term] id: UBERON:0001844 @@ -183026,8 +183196,8 @@ is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001839 {source="FMA", source="VHOG", source="XAO", source="ncit"} ! bony labyrinth relationship: RO:0000086 PATO:0000404 {gci_relation="part_of", gci_filler="NCBITaxon:32525", source="Wikipedia"} ! has quality coiled relationship: RO:0002433 UBERON:0001846 ! contributes to morphology of internal ear -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI [Term] id: UBERON:0001845 @@ -183096,7 +183266,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001690 ! ear relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI [Term] id: UBERON:0001848 @@ -183144,7 +183314,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001846 {source="FMA", source="MA"} ! internal ear relationship: RO:0001025 UBERON:0004637 ! located in otic capsule relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png" xsd:anyURI [Term] id: UBERON:0001850 @@ -183252,7 +183422,7 @@ xref: Wikipedia:Saccule xref: XAO:0000196 xref: ZFA:0000428 is_a: UBERON:0002518 {source="Wikipedia", source="ZFA"} ! otolith organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI [Term] id: UBERON:0001855 @@ -183290,7 +183460,7 @@ xref: Wikipedia:Cochlear_duct is_a: UBERON:0000025 ! tube is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002499 {source="FMA", source="MA"} ! cochlear labyrinth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI property_value: IAO:0000116 "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string [Term] @@ -183447,7 +183617,7 @@ is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000955 ! brain relationship: BSPO:0000126 UBERON:0001893 {source="FMA-abduced-lr"} ! telencephalon relationship: part_of UBERON:0001893 ! telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI [Term] id: UBERON:0001870 @@ -183476,7 +183646,7 @@ is_a: UBERON:0016529 ! cortex of cerebral lobe intersection_of: UBERON:0016529 ! cortex of cerebral lobe intersection_of: part_of UBERON:0016525 ! frontal lobe relationship: part_of UBERON:0016525 ! frontal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -183513,7 +183683,7 @@ xref: UMLS:C1268978 {source="BIRNLEX:1160"} xref: Wikipedia:Temporal_lobe is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -183548,7 +183718,7 @@ xref: Wikipedia:Parietal_lobe is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere relationship: adjacent_to UBERON:0001871 ! temporal lobe relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -183592,7 +183762,7 @@ xref: Wikipedia:Caudate_nucleus is_a: UBERON:0009663 ! telencephalic nucleus relationship: part_of UBERON:0005383 {source="MA"} ! caudate-putamen relationship: RO:0002433 UBERON:0005383 ! contributes to morphology of caudate-putamen -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Telencephalon-Horiconatal.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Telencephalon-Horiconatal.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -183629,7 +183799,7 @@ is_a: UBERON:0009663 ! telencephalic nucleus relationship: part_of UBERON:0001869 {source="FMA"} ! cerebral hemisphere relationship: part_of UBERON:0005383 ! caudate-putamen relationship: RO:0002433 UBERON:0005383 ! contributes to morphology of caudate-putamen -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI property_value: IAO:0000116 "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -183686,7 +183856,7 @@ is_a: UBERON:0002420 {source="FMA"} ! basal ganglion is_a: UBERON:0005401 ! cerebral hemisphere gray matter relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0001871 {source="BTO"} ! temporal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Amyg.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Amyg.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -183725,7 +183895,7 @@ relationship: part_of UBERON:0001882 {gci_relation="part_of", gci_filler="NCBITa relationship: part_of UBERON:0001883 {gci_relation="part_of", gci_filler="NCBITaxon:9989", source="MP"} ! olfactory tubercle relationship: RO:0002433 UBERON:0001882 ! contributes to morphology of nucleus accumbens relationship: RO:0002433 UBERON:0001883 ! contributes to morphology of olfactory tubercle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Islands_of_Calleja_Rat.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Islands_of_Calleja_Rat.jpg" xsd:anyURI [Term] id: UBERON:0001882 @@ -183768,7 +183938,7 @@ relationship: part_of UBERON:0000349 {source="FMA", source="GO"} ! limbic system relationship: part_of UBERON:0001869 ! cerebral hemisphere relationship: part_of UBERON:0005403 {source="MA"} ! ventral striatum relationship: RO:0002433 UBERON:0005403 ! contributes to morphology of ventral striatum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:8782 {source="ISBN:0471888893"} property_value: RO:0002175 NCBITaxon:9606 @@ -183801,7 +183971,7 @@ xref: Wikipedia:Olfactory_tubercle is_a: UBERON:0009663 ! telencephalic nucleus relationship: part_of UBERON:0002894 {source="EHDAA2-inferred", source="MA", source="VHOG", source="Wikipedia"} ! olfactory cortex relationship: RO:0002433 UBERON:0002894 ! contributes to morphology of olfactory cortex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI [Term] id: UBERON:0001884 @@ -183832,7 +184002,7 @@ intersection_of: UBERON:0001021 ! nerve intersection_of: RO:0002134 UBERON:0001103 ! innervates diaphragm relationship: RO:0002134 UBERON:0001103 ! innervates diaphragm relationship: RO:0002380 UBERON:0000962 ! branching part of nerve of cervical vertebra -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -183875,7 +184045,7 @@ xref: Wikipedia:Dentate_gyrus is_a: UBERON:0000200 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! gyrus is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002421 {source="MA"} ! hippocampal formation -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg" xsd:anyURI [Term] id: UBERON:0001886 @@ -183920,7 +184090,7 @@ is_a: UBERON:0036303 ! vasculature of central nervous system relationship: part_of UBERON:0004086 ! brain ventricle relationship: part_of UBERON:0005283 ! tela choroidea relationship: RO:0002433 UBERON:0003947 ! contributes to morphology of brain ventricle/choroid plexus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere" xsd:string [Term] @@ -183959,7 +184129,7 @@ is_a: UBERON:0034730 ! olfactory tract linking bulb to ipsilateral dorsal telenc intersection_of: UBERON:0002265 ! olfactory tract intersection_of: overlaps UBERON:0002894 ! olfactory cortex relationship: overlaps UBERON:0002894 ! olfactory cortex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI [Term] id: UBERON:0001889 @@ -184019,7 +184189,7 @@ disjoint_from: UBERON:0002298 ! brainstem relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0006240 ! immediate transformation of future forebrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -184069,7 +184239,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre relationship: RO:0002254 UBERON:0003849 ! has developmental contribution from mesencephalic neural crest relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0009616 {source="Bgee:AN"} ! immediate transformation of presumptive midbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI property_value: IAO:0000116 "developmental relationships need revised" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -184212,7 +184382,7 @@ relationship: part_of UBERON:0001890 ! forebrain relationship: RO:0002254 UBERON:0003851 ! has developmental contribution from diencephalon neural crest relationship: RO:0002433 UBERON:0001890 ! contributes to morphology of forebrain relationship: RO:0002495 UBERON:0006222 ! immediate transformation of future diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001895 @@ -184246,7 +184416,7 @@ xref: Wikipedia:Metencephalon is_a: UBERON:0004733 ! segmental subdivision of hindbrain relationship: RO:0002433 UBERON:0002028 ! contributes to morphology of hindbrain relationship: RO:0002495 UBERON:0010092 ! immediate transformation of future metencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001896 @@ -184301,7 +184471,7 @@ relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -184352,7 +184522,7 @@ is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0010225 {source="FMA-abduced-lr"} ! thalamic complex relationship: part_of UBERON:0010225 ! thalamic complex relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -184405,9 +184575,9 @@ relationship: capable_of GO:0046883 {source="WP"} ! regulation of hormone secret relationship: part_of UBERON:0000349 ! limbic system relationship: part_of UBERON:0010225 ! thalamic complex relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} property_value: RO:0002175 NCBITaxon:7742 property_value: RO:0002175 NCBITaxon:9606 @@ -184459,7 +184629,7 @@ xref: ZFA:0000509 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001897 ! dorsal plus ventral thalamus relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Epithalamus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Epithalamus.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:7742 property_value: RO:0002175 NCBITaxon:9606 @@ -184589,9 +184759,9 @@ relationship: has_part CL:0000652 ! pinealocyte relationship: has_part CL:0002220 ! interstitial cell of pineal gland relationship: part_of UBERON:0015238 {source="ZFA", source="various"} ! pineal complex relationship: RO:0002433 UBERON:0001899 ! contributes to morphology of epithalamus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:117569 {source="Hardisty, p. 310"} property_value: RO:0002175 NCBITaxon:9606 @@ -184637,9 +184807,9 @@ relationship: part_of UBERON:0002104 ! visual system relationship: part_of UBERON:0003931 ! diencephalic white matter relationship: RO:0002134 UBERON:0000966 ! innervates retina relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -184686,7 +184856,7 @@ relationship: capable_of GO:0007595 ! lactation relationship: produces UBERON:0001913 ! milk relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia relationship: RO:0002202 UBERON:0005333 ! develops from mammary bud -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI property_value: IAO:0000116 "Originally this was classified as a female reproductive structure, as it was in the MP in 2011" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -184888,7 +185058,7 @@ xref: Wikipedia:Lateral_geniculate_body is_a: UBERON:0015233 ! nucleus of dorsal thalamus relationship: part_of UBERON:0002704 {source="FMA"} ! metathalamus relationship: RO:0002433 UBERON:0001897 ! contributes to morphology of dorsal plus ventral thalamus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} property_value: RO:0002175 NCBITaxon:9606 @@ -184933,7 +185103,7 @@ xref: ZFA:0000470 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001898 {gci_relation="part_of", gci_filler="NCBITaxon:32524", source="PMC4038951"} ! hypothalamus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI property_value: RO:0002175 NCBITaxon:7742 [Term] @@ -184981,8 +185151,8 @@ xref: Wikipedia:Paraventricular_nucleus_of_hypothalamus is_a: UBERON:0006568 ! hypothalamic nucleus relationship: part_of UBERON:0002271 ! periventricular zone of hypothalamus relationship: RO:0002433 UBERON:0001898 ! contributes to morphology of hypothalamus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg" xsd:anyURI [Term] id: UBERON:0001932 @@ -185028,7 +185198,7 @@ xref: Wikipedia:Arcuate_nucleus is_a: UBERON:0006568 ! hypothalamic nucleus relationship: part_of UBERON:0002271 ! periventricular zone of hypothalamus relationship: part_of UBERON:0002555 {source="NIFSTD"} ! intermediate hypothalamic region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI [Term] id: UBERON:0001943 @@ -185070,7 +185240,7 @@ is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem relationship: RO:0002202 UBERON:0010285 {source="ZFA"} ! develops from midbrain basal plate -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -185151,7 +185321,7 @@ is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0000956 ! cerebral cortex relationship: RO:0002160 NCBITaxon:7742 {source="Wikipedia"} ! only in taxon Vertebrata relationship: RO:0002433 UBERON:0000956 ! contributes to morphology of cerebral cortex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg" xsd:anyURI [Term] id: UBERON:0001951 @@ -185241,7 +185411,7 @@ relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0002421 {source="ABA"} ! hippocampal formation relationship: part_of UBERON:0002600 {source="FMA"} ! limbic lobe relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! only in taxon Mammalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png" xsd:anyURI [Term] id: UBERON:0001955 @@ -185295,8 +185465,8 @@ relationship: has_part CL:0019002 ! tracheobronchial chondrocyte relationship: part_of UBERON:0002185 ! bronchus relationship: RO:0002433 UBERON:0002185 ! contributes to morphology of bronchus relationship: RO:0002473 UBERON:0001994 {source="MP"} ! composed primarily of hyaline cartilage tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0001957 @@ -185347,8 +185517,8 @@ is_a: UBERON:0002051 ! epithelium of bronchiole intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002187 ! terminal bronchiole relationship: part_of UBERON:0002187 ! terminal bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0001959 @@ -185373,7 +185543,7 @@ xref: Wikipedia:White_pulp is_a: UBERON:1000023 ! spleen pulp relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen relationship: RO:0002473 CL:0000542 ! composed primarily of lymphocyte -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -185495,7 +185665,7 @@ is_a: UBERON:0000463 ! organism substance relationship: has_part CL:0000019 ! sperm relationship: has_part UBERON:0006530 ! seminal fluid relationship: output_of GO:0042713 ! sperm ejaculation -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg" xsd:anyURI [Term] id: UBERON:0001969 @@ -185758,7 +185928,7 @@ is_a: UBERON:0003920 ! venous blood vessel is_a: UBERON:8410081 ! blood microvessel relationship: RO:0002176 UBERON:0001638 ! connects vein relationship: RO:0002176 UBERON:0001982 ! connects capillary -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -185791,7 +185961,7 @@ intersection_of: RO:0002176 UBERON:0001982 ! connects capillary relationship: RO:0002176 UBERON:0001637 ! connects artery relationship: RO:0002176 UBERON:0001982 ! connects capillary relationship: RO:0002433 UBERON:0001637 ! contributes to morphology of artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI [Term] id: UBERON:0001981 @@ -185841,7 +186011,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -185880,7 +186050,7 @@ intersection_of: RO:0002176 UBERON:0001979 ! connects venule intersection_of: RO:0002176 UBERON:0001980 ! connects arteriole relationship: RO:0002176 UBERON:0001979 ! connects venule relationship: RO:0002176 UBERON:0001980 ! connects arteriole -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string @@ -185916,7 +186086,7 @@ is_a: UBERON:0000333 ! intestinal gland relationship: RO:0000086 PATO:0002299 {source="Wikipedia:Tubular_gland"} ! has quality tubular relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda relationship: RO:0002433 UBERON:0001242 ! contributes to morphology of intestinal mucosa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI property_value: seeAlso UBERON:2005256 [Term] @@ -185974,7 +186144,7 @@ intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0000964 ! cornea relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186042,9 +186212,9 @@ relationship: RO:0002160 NCBITaxon:32525 {source="https://github.com/obophenotyp relationship: RO:0002202 UBERON:0000995 {source="ISBN:0073040584"} ! develops from uterus relationship: RO:0002202 UBERON:0003124 {source="Wikipedia"} ! develops from chorion membrane relationship: RO:0002202 UBERON:0004340 {source="ISBN:0073040584"} ! develops from allantois -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186132,7 +186302,7 @@ is_a: UBERON:0013754 ! integumentary system layer relationship: part_of UBERON:0002067 ! dermis relationship: RO:0002473 UBERON:0006815 {source="WP"} ! composed primarily of areolar connective tissue relationship: RO:0002473 UBERON:0011822 {source="FMA-text"} ! composed primarily of dense irregular connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG" xsd:anyURI property_value: IAO:0000116 "todo - check tissue composition" xsd:string [Term] @@ -186184,8 +186354,8 @@ xref: Wikipedia:Hyaline_cartilage xref: XAO:0004029 is_a: UBERON:0002418 {source="FMA"} ! cartilage tissue relationship: RO:0002473 GO:0005585 {source="VSAO-text-def"} ! composed primarily of collagen type II trimer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI [Term] id: UBERON:0001995 @@ -186208,7 +186378,7 @@ xref: Wikipedia:Fibrocartilage xref: XAO:0004028 is_a: UBERON:0002418 ! cartilage tissue relationship: has_part GO:0005584 ! collagen type I trimer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png" xsd:anyURI [Term] id: UBERON:0001996 @@ -186235,7 +186405,7 @@ is_a: UBERON:0011589 {source="VSAO"} ! non-mineralized cartilage tissue relationship: has_part GO:0071953 {source="Wikipedia"} ! elastic fiber relationship: RO:0000086 PATO:0001544 ! has quality flexible relationship: RO:0002202 UBERON:0005863 {source="VSAO"} ! develops from cartilaginous condensation -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray904.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray904.png" xsd:anyURI [Term] id: UBERON:0001997 @@ -186288,7 +186458,7 @@ relationship: part_of UBERON:0005386 ! olfactory segment of nasal mucosa relationship: RO:0002433 UBERON:0005725 ! contributes to morphology of olfactory system relationship: RO:0002495 UBERON:2001431 ! immediate transformation of primitive olfactory epithelium relationship: site_of GO:0022008 {source="NCBIBook:NBK55982"} ! neurogenesis -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png" xsd:anyURI [Term] id: UBERON:0002001 @@ -186375,7 +186545,7 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002194 ! capsule of lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186397,8 +186567,8 @@ intersection_of: part_of UBERON:0000029 ! lymph node relationship: has_part UBERON:0009744 ! lymph node medullary sinus relationship: has_part UBERON:0009745 ! lymph node medullary cord relationship: part_of UBERON:0000029 ! lymph node -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186425,7 +186595,7 @@ is_a: UBERON:0001816 ! autonomic nerve plexus intersection_of: UBERON:0001816 ! autonomic nerve plexus intersection_of: RO:0002134 UBERON:0000948 ! innervates heart relationship: RO:0002134 UBERON:0000948 ! innervates heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI [Term] id: UBERON:0002011 @@ -186446,7 +186616,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001112 ! supplies latissimus dorsi muscle relationship: RO:0002170 UBERON:0001397 ! connected to subscapular artery relationship: RO:0002178 UBERON:0001112 ! supplies latissimus dorsi muscle -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186493,9 +186663,9 @@ relationship: RO:0002178 UBERON:0002048 ! supplies lung relationship: RO:0002202 UBERON:0002061 {source="Wikipedia"} ! develops from truncus arteriosus relationship: RO:0002202 UBERON:0003123 {source="EHDAA2", source="XAO"} ! develops from pharyngeal arch artery 6 relationship: RO:0002202 UBERON:0005339 {source="EHDAA2"} ! develops from outflow tract pulmonary component -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186524,11 +186694,11 @@ intersection_of: UBERON:0011824 ! fibrous connective tissue intersection_of: bounding_layer_of UBERON:0002113 ! kidney relationship: bounding_layer_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186566,9 +186736,9 @@ relationship: part_of UBERON:0008886 ! pulmonary vascular system relationship: RO:0002170 UBERON:0002079 ! connected to left cardiac atrium relationship: RO:0002179 UBERON:0002048 ! drains lung relationship: RO:0002202 UBERON:0002061 ! develops from truncus arteriosus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186597,7 +186767,7 @@ xref: VHOG:0000656 xref: XAO:0000392 is_a: UBERON:0001638 {source="FMA"} ! vein relationship: part_of UBERON:0005806 ! portal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186639,8 +186809,8 @@ is_a: UBERON:0012275 ! meso-epithelium relationship: has_part CL:0000214 ! synovial cell relationship: part_of UBERON:0002217 {source="EHDAA2"} ! synovial joint relationship: RO:0002371 UBERON:0001484 {source="GAID"} ! attached to articular capsule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png" xsd:anyURI [Term] id: UBERON:0002019 @@ -186675,7 +186845,6 @@ xref: EMAPA:17265 xref: FMA:6720 xref: FMA:80284 xref: GAID:825 -xref: HBA:9340 xref: MA:0001088 xref: MBA:717 xref: MESH:D000055 @@ -186692,7 +186861,7 @@ intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus relationship: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI [Term] id: UBERON:0002020 @@ -186727,7 +186896,7 @@ xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002025 @@ -186844,8 +187013,8 @@ relationship: BFO:0000067 GO:0031424 ! contains process keratinization relationship: BSPO:0000108 UBERON:0002069 ! stratum granulosum of epidermis relationship: has_part CL:0002153 {source="FMA"} ! corneocyte relationship: part_of UBERON:0001003 ! skin epidermis -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -186892,7 +187061,7 @@ relationship: overlaps UBERON:0002298 ! brainstem relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} property_value: RO:0002175 NCBITaxon:9606 @@ -186958,7 +187127,7 @@ relationship: part_of UBERON:0000310 {gci_relation="part_of", gci_filler="NCBITa relationship: part_of UBERON:0001911 ! mammary gland relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria relationship: RO:0002202 UBERON:0008425 {source="Stedmans"} ! develops from mammary ridge -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/1873" xsd:string [Term] @@ -187097,7 +187266,7 @@ relationship: part_of UBERON:0001895 {source="FMA", source="MA"} ! metencephalon relationship: RO:0002160 NCBITaxon:7742 {source="ISBN:0471888893"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0006215 ! develops from rhombic lip relationship: RO:0002433 UBERON:0001895 ! contributes to morphology of metencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:117565 {source="ISBN:0471888893"} property_value: RO:0002175 NCBITaxon:117569 {source="ISBN:0471888893"} property_value: RO:0002175 NCBITaxon:9606 @@ -187145,9 +187314,9 @@ relationship: BSPO:0000126 UBERON:0001891 {source="FMA-abduced-lr"} ! midbrain relationship: part_of UBERON:0002420 {source="NIF"} ! basal ganglion relationship: RO:0002433 UBERON:0001891 ! contributes to morphology of midbrain relationship: RO:0002433 UBERON:0010011 ! contributes to morphology of collection of basal ganglia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -187178,7 +187347,7 @@ intersection_of: RO:0002178 UBERON:0002048 ! supplies lung relationship: has_part UBERON:0004848 ! respiratory system arterial endothelium relationship: has_part UBERON:0012416 ! respiratory system arterial smooth muscle relationship: RO:0002178 UBERON:0002048 ! supplies lung -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -187253,8 +187422,8 @@ relationship: capable_of GO:0036161 {source="Wikipedia"} ! calcitonin secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis relationship: RO:0002160 NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! only in taxon Chordata relationship: RO:0002494 UBERON:0007689 ! transformation of thyroid diverticulum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI [Term] id: UBERON:0002047 @@ -187332,8 +187501,8 @@ relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI @@ -188317,9 +188486,9 @@ intersection_of: adjacent_to UBERON:0002080 ! heart right ventricle intersection_of: adjacent_to UBERON:0002084 ! heart left ventricle relationship: adjacent_to UBERON:0002080 ! heart right ventricle relationship: adjacent_to UBERON:0002084 ! heart left ventricle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -188345,7 +188514,7 @@ xref: UMLS:C0025474 {source="ncithesaurus:Mesentery"} xref: Wikipedia:Mesentery#Mesentery_.28general.29 is_a: UBERON:0000042 ! serous membrane relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png" xsd:anyURI [Term] id: UBERON:0002097 @@ -188383,11 +188552,11 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002199 ! integument relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer relationship: RO:0002473 UBERON:0000014 ! composed primarily of zone of skin -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Skin.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Skin.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -188603,7 +188772,7 @@ intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0000154 ! posterior region of body relationship: RO:0002202 UBERON:0005418 ! develops from hindlimb bud relationship: RO:0002551 UBERON:0001441 ! has skeleton hindlimb skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png" xsd:anyURI [Term] id: UBERON:0002104 @@ -188654,7 +188823,7 @@ xref: XAO:0003195 xref: ZFA:0001138 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007605 ! sensory perception of sound -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg" xsd:anyURI [Term] id: UBERON:0002106 @@ -188694,10 +188863,10 @@ is_a: UBERON:0005057 ! immune organ is_a: UBERON:0017672 ! abdominal viscera relationship: RO:0002160 NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! only in taxon Gnathostomata relationship: RO:0002202 UBERON:0006293 ! develops from spleen primordium -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Spleen.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Spleen.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -188752,9 +188921,9 @@ relationship: RO:0002433 UBERON:0002423 ! contributes to morphology of hepatobil relationship: site_of GO:0002384 ! hepatic immune response relationship: site_of GO:0005978 ! glycogen biosynthetic process relationship: site_of GO:0005980 ! glycogen catabolic process -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -188800,9 +188969,9 @@ is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0000160 ! intestine relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -188872,8 +189041,8 @@ relationship: part_of UBERON:0002294 ! biliary system relationship: RO:0002202 UBERON:0004912 ! develops from biliary bud relationship: RO:0002202 UBERON:0006242 ! develops from gallbladder primordium relationship: RO:0002433 UBERON:0001173 ! contributes to morphology of biliary tree -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:10114 {source="ISBN:9780120749034"} property_value: RO:0002161 NCBITaxon:8801 {source="GOC:mr", source="ISBN:9781840761122"} property_value: RO:0002161 NCBITaxon:8930 {source="GOC:mr", source="ISBN:9781840761122"} @@ -188974,9 +189143,9 @@ relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2804-127X property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:contributor https://orcid.org/0000-0003-2804-127X [Term] id: UBERON:0002114 @@ -189014,9 +189183,9 @@ relationship: BSPO:0001106 UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine relationship: RO:0002150 UBERON:0001166 ! continuous with pylorus relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:7955 {source="ZFA:0000348"} property_value: RO:0002175 NCBITaxon:9606 @@ -189054,9 +189223,9 @@ is_a: UBERON:0004921 ! subdivision of digestive tract relationship: part_of UBERON:0002108 ! small intestine relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI property_value: IAO:0000116 "TODO consider ZFA:0001323 mid intestine, see also small intestine" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -189095,9 +189264,9 @@ xref: XAO:0000237 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: part_of UBERON:0002108 ! small intestine relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI property_value: IAO:0000116 "TODO consider ZFA:0000706 posterior intestine, see also colon" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -189306,7 +189475,7 @@ is_a: UBERON:0007245 ! nuclear complex of neuraxis is_a: UBERON:0019263 ! gray matter of hindbrain relationship: part_of UBERON:0003023 {source="NIFSTD"} ! pontine tegmentum relationship: part_of UBERON:0016490 ! auditory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png" xsd:anyURI [Term] id: UBERON:0002129 @@ -189348,7 +189517,7 @@ is_a: UBERON:0019263 ! gray matter of hindbrain relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: part_of UBERON:0002037 ! cerebellum relationship: RO:0002433 UBERON:0002037 ! contributes to morphology of cerebellum -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189388,7 +189557,7 @@ relationship: has_part CL:0000065 ! ependymal cell relationship: part_of UBERON:0002314 {source="MA"} ! midbrain tectum relationship: part_of UBERON:0011357 ! Reissner's fiber relationship: produces PR:000015658 ! SCO-spondin -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray715.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray715.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:7742 {source="multiple"} [Term] @@ -189441,7 +189610,7 @@ is_a: UBERON:0009662 ! hindbrain nucleus is_a: UBERON:8440015 ! noradrenergic cell groups relationship: capable_of GO:0048243 ! norepinephrine secretion relationship: part_of UBERON:0003023 ! pontine tegmentum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png" xsd:anyURI property_value: IAO:0000116 "TODO - check ZFA/pons. also GO says part of dorsorostral pons" xsd:string [Term] @@ -189474,7 +189643,7 @@ is_a: UBERON:0004133 ! salivatory nucleus is_a: UBERON:0007635 ! nucleus of medulla oblongata relationship: part_of UBERON:0003023 ! pontine tegmentum relationship: RO:0002495 UBERON:0010125 ! immediate transformation of future superior salivatory nucleus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png" xsd:anyURI [Term] id: UBERON:0002165 @@ -189517,7 +189686,7 @@ is_a: UBERON:0002523 ! tunica intima is_a: UBERON:0005983 ! heart layer relationship: has_part UBERON:0005316 ! endocardial endothelium relationship: RO:0002495 UBERON:0007280 {source="Bgee:AN"} ! immediate transformation of presumptive endocardium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png" xsd:anyURI [Term] id: UBERON:0002166 @@ -189571,9 +189740,9 @@ is_a: UBERON:0002048 ! lung intersection_of: UBERON:0002048 ! lung intersection_of: BSPO:0000121 UBERON:0000170 ! pair of lungs relationship: BSPO:0000121 UBERON:0000170 ! pair of lungs -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0002168 @@ -189596,9 +189765,9 @@ is_a: UBERON:0002048 ! lung intersection_of: UBERON:0002048 ! lung intersection_of: BSPO:0000120 UBERON:0000170 ! pair of lungs relationship: BSPO:0000120 UBERON:0000170 ! pair of lungs -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0002169 @@ -189648,7 +189817,7 @@ xref: UMLS:C0391892 {source="ncithesaurus:Alveolar_Duct"} xref: Wikipedia:Alveolar_duct is_a: UBERON:0000117 ! respiratory tube relationship: part_of UBERON:0006524 ! alveolar system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8f/Gray975.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8f/Gray975.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189676,7 +189845,7 @@ xref: ZFA:0000605 is_a: UBERON:0006127 ! funiculus of spinal cord is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0002318 {source="FMA-abduced-lr"} ! white matter of spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI [Term] id: UBERON:0002183 @@ -189713,7 +189882,7 @@ relationship: has_part UBERON:0001956 ! cartilage of bronchus relationship: has_part UBERON:0004242 ! bronchus smooth muscle relationship: has_part UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:0000101 {source="FMA"} ! lobe of lung -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189746,9 +189915,9 @@ relationship: has_part UBERON:8410043 ! bronchus submucosal gland relationship: overlaps UBERON:8600017 ! bronchopulmonary segment relationship: part_of UBERON:0000101 {source="FMA"} ! lobe of lung relationship: proximally_connected_to UBERON:0002183 ! lobar bronchus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189784,9 +189953,9 @@ xref: XAO:0000121 is_a: UBERON:0000117 ! respiratory tube relationship: part_of UBERON:0007196 ! tracheobronchial tree relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:8507 {source="Wikipedia"} property_value: RO:0002175 NCBITaxon:9606 @@ -189817,7 +189986,7 @@ xref: Wikipedia:Bronchiole is_a: UBERON:0000117 ! respiratory tube relationship: part_of UBERON:0002048 {source="MA"} ! lung relationship: RO:0002380 UBERON:0007196 {source="FMA"} ! branching part of tracheobronchial tree -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI [Term] id: UBERON:0002187 @@ -189842,7 +190011,7 @@ is_a: UBERON:0002186 ! bronchiole relationship: distally_connected_to UBERON:0002188 ! respiratory bronchiole relationship: distally_connected_to UBERON:0008874 ! pulmonary acinus relationship: part_of UBERON:0010369 ! secondary pulmonary lobule -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189868,7 +190037,7 @@ relationship: distally_connected_to UBERON:0002173 ! pulmonary alveolar duct relationship: part_of UBERON:0008874 {source="ISBN:0123813611"} ! pulmonary acinus relationship: proximally_connected_to UBERON:0002187 ! terminal bronchiole relationship: RO:0002433 UBERON:0008874 ! contributes to morphology of pulmonary acinus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189933,7 +190102,7 @@ xref: Wikipedia:Subiculum is_a: UBERON:0002616 ! regional part of brain relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: part_of UBERON:0002421 {source="NIFSTD"} ! hippocampal formation -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Hippocampus.gif" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Hippocampus.gif" xsd:anyURI [Term] id: UBERON:0002193 @@ -189972,9 +190141,9 @@ intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0000029 ! lymph node relationship: bounding_layer_of UBERON:0000029 ! lymph node relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/92/Lymphknoten_(Schwein).jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/92/Lymphknoten_(Schwein).jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -189997,7 +190166,7 @@ is_a: UBERON:0000440 ! trabecula intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -190062,7 +190231,7 @@ relationship: part_of UBERON:0000007 ! pituitary gland relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0009122 {source="NCBIBook:NBK53175", source="ZFA"} ! develops from adenohypophyseal placode relationship: RO:0002433 UBERON:0000007 ! contributes to morphology of pituitary gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png" xsd:anyURI [Term] id: UBERON:0002198 @@ -190125,7 +190294,7 @@ relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion relationship: part_of UBERON:0000007 {source="ZFA"} ! pituitary gland relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG" xsd:anyURI property_value: IAO:0000116 "request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'" xsd:string {source="http://syllabus.med.unc.edu/courseware/embryo_images/"} property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} @@ -190263,8 +190432,8 @@ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -190348,7 +190517,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002272 {source="ABA"} ! medial zone of hypothalamus relationship: part_of UBERON:0002770 {source="GO definition"} ! posterior hypothalamic region relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:117569 {source="Hardisty, p. 320-1"} property_value: RO:0002175 NCBITaxon:9606 @@ -190392,6 +190561,7 @@ id: UBERON:0002211 name: nerve root namespace: uberon def: "A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/286] +subset: human_reference_atlas subset: uberon_slim synonym: "initial segment of nerve" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "radix nervi" EXACT OMO:0003011 [] @@ -190406,6 +190576,7 @@ is_a: UBERON:0000122 ! neuron projection bundle relationship: extends_fibers_into UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001021 ! nerve property_value: IAO:0000116 "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002212 @@ -190502,7 +190673,7 @@ intersection_of: UBERON:0000054 ! macula intersection_of: part_of UBERON:0001853 ! utricle of membranous labyrinth relationship: part_of UBERON:0001853 ! utricle of membranous labyrinth relationship: RO:0002433 UBERON:0001853 ! contributes to morphology of utricle of membranous labyrinth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI [Term] id: UBERON:0002215 @@ -190524,7 +190695,7 @@ is_a: UBERON:0002213 ! cartilaginous joint intersection_of: UBERON:0002209 ! fibrous joint intersection_of: RO:0002473 UBERON:0001994 ! composed primarily of hyaline cartilage tissue relationship: RO:0002473 UBERON:0001994 ! composed primarily of hyaline cartilage tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png" xsd:anyURI property_value: IAO:0000116 "consider adding link to hyaline cartilage" xsd:string property_value: IAO:0000116 "WP considers epiphyseal plates as subtypes of this" xsd:string @@ -190542,7 +190713,7 @@ xref: SCTID:1584001 xref: Wikipedia:Symphysis is_a: UBERON:0002209 {source="MA"} ! fibrous joint is_a: UBERON:0002213 {source="FMA"} ! cartilaginous joint -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png" xsd:anyURI property_value: IAO:0000116 "consider adding fibrocartilage class" xsd:string [Term] @@ -190630,8 +190801,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002227 @@ -190672,8 +190843,8 @@ relationship: has_part CL:0000202 ! auditory hair cell relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth relationship: RO:0001025 UBERON:0002295 {source="Wikipedia:Scala_media"} ! located in scala media relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:40674 [Term] @@ -190752,7 +190923,7 @@ is_a: UBERON:0002228 ! rib intersection_of: UBERON:0002228 ! rib intersection_of: RO:0002170 UBERON:0000975 ! connected to sternum relationship: RO:0002170 UBERON:0000975 ! connected to sternum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png" xsd:anyURI [Term] id: UBERON:0002240 @@ -190813,9 +190984,9 @@ relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -190869,7 +191040,7 @@ relationship: has_part UBERON:0011860 ! collection of collagen fibrils relationship: part_of UBERON:0001066 ! intervertebral disk relationship: RO:0002202 UBERON:0002328 ! develops from notochord relationship: RO:0002433 UBERON:0001066 ! contributes to morphology of intervertebral disk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI [Term] id: UBERON:0002255 @@ -190909,7 +191080,7 @@ relationship: RO:0000086 PATO:0000588 {gci_relation="part_of", gci_filler="NCBIT relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii relationship: RO:0002202 UBERON:0003050 {source="Wikipedia"} ! develops from olfactory placode relationship: RO:0002254 UBERON:0009714 {source="EHDAA2-abduced"} ! has developmental contribution from intermaxillary process -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png" xsd:anyURI [Term] id: UBERON:0002256 @@ -190963,7 +191134,7 @@ relationship: capable_of_part_of GO:0019230 {source="GO"} ! proprioception relationship: has_part CL:0000101 ! sensory neuron relationship: part_of UBERON:0002315 ! gray matter of spinal cord relationship: RO:0002433 UBERON:0002315 ! contributes to morphology of gray matter of spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI [Term] id: UBERON:0002257 @@ -191052,7 +191223,7 @@ xref: ZFA:0000652 is_a: UBERON:0009623 {source="FMA"} ! spinal nerve root relationship: capable_of_part_of GO:0019230 {source="Wikipedia"} ! proprioception relationship: extends_fibers_into UBERON:0000044 ! dorsal root ganglion -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002264 @@ -191101,10 +191272,10 @@ relationship: capable_of GO:0007608 ! sensory perception of smell relationship: has_part CL:0000626 {source="ZFA"} ! olfactory granule cell relationship: part_of UBERON:0005366 ! olfactory lobe relationship: RO:0002433 UBERON:0005366 ! contributes to morphology of olfactory lobe -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -191139,7 +191310,7 @@ intersection_of: UBERON:0007702 ! tract of brain intersection_of: overlaps UBERON:0002264 ! olfactory bulb relationship: overlaps UBERON:0002264 ! olfactory bulb relationship: part_of UBERON:0011299 ! white matter of telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -191158,7 +191329,7 @@ synonym: "organum olfactorium" RELATED [BTO:0001772] synonym: "primary olfactory organ" NARROW [] xref: AAO:0010180 xref: BTO:0001772 -xref: FBbt:00005158 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005158 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:77659 xref: VHOG:0000287 xref: XAO:0000273 @@ -191228,7 +191399,7 @@ xref: SCTID:361552007 xref: Wikipedia:Reticular_formation is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002298 ! brainstem -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png" xsd:anyURI [Term] id: UBERON:0002276 @@ -191250,7 +191421,7 @@ xref: Wikipedia:Limbus_laminae_spiralis is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray930.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray930.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -191302,7 +191473,7 @@ is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001855 {source="FMA", source="MA"} ! cochlear duct of membranous labyrinth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI [Term] id: UBERON:0002285 @@ -191356,7 +191527,7 @@ intersection_of: UBERON:0004086 ! brain ventricle intersection_of: part_of UBERON:0001893 ! telencephalon relationship: part_of UBERON:0001893 ! telencephalon relationship: RO:0002494 UBERON:0009676 ! transformation of early telencephalic vesicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -191435,7 +191606,7 @@ relationship: part_of UBERON:0002240 {source="MA"} ! spinal cord relationship: part_of UBERON:0005281 {source="FMA"} ! ventricular system of central nervous system relationship: RO:0002202 UBERON:0001049 ! develops from neural tube relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -191471,7 +191642,7 @@ relationship: capable_of GO:0006699 ! bile acid biosynthetic process relationship: capable_of GO:0015721 ! bile acid and bile salt transport relationship: has_part UBERON:0001173 ! biliary tree relationship: part_of UBERON:0002423 ! hepatobiliary system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI [Term] id: UBERON:0002295 @@ -191490,7 +191661,7 @@ is_a: UBERON:0011060 {source="MA"} ! perilymphatic channel is_a: UBERON:0013685 ! foramen of skull relationship: part_of UBERON:0001844 {source="FMA"} ! cochlea relationship: RO:0002433 UBERON:0001844 ! contributes to morphology of cochlea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI property_value: IAO:0000116 "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string [Term] @@ -191517,7 +191688,7 @@ xref: ZFA:0005130 is_a: UBERON:0006598 ! presumptive structure relationship: part_of UBERON:0009664 {source="EHDAA2"} ! gut mesentery relationship: RO:0002387 UBERON:0002095 ! has potential to develop into mesentery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png" xsd:anyURI [Term] id: UBERON:0002298 @@ -191561,7 +191732,7 @@ relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum relationship: RO:0002150 UBERON:0002240 ! continuous with spinal cord relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI [Term] id: UBERON:0002299 @@ -191600,7 +191771,7 @@ relationship: part_of UBERON:0006524 {source="MA"} ! alveolar system relationship: part_of UBERON:0008874 ! pulmonary acinus relationship: RO:0002160 NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! only in taxon Mammalia relationship: RO:0002433 UBERON:0008874 ! contributes to morphology of pulmonary acinus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -191825,7 +191996,7 @@ is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: part_of UBERON:0000052 ! fornix of brain relationship: part_of UBERON:0001954 {source="MA", source="NIFSTD"} ! Ammon's horn relationship: part_of UBERON:0011299 ! white matter of telencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray749.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray749.png" xsd:anyURI [Term] id: UBERON:0002313 @@ -191898,7 +192069,7 @@ xref: Wikipedia:Midbrain_tectum is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001891 ! midbrain relationship: RO:0002202 UBERON:0005882 {source="Wikipedia"} ! develops from neural tube alar plate -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray685.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray685.png" xsd:anyURI [Term] id: UBERON:0002315 @@ -191965,8 +192136,8 @@ xref: Wikipedia:White_matter xref: ZFA:0001682 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: RO:0002473 UBERON:0006135 ! composed primarily of myelinated nerve fiber -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002318 @@ -192096,7 +192267,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -192235,7 +192406,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -192277,7 +192448,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -192345,8 +192516,8 @@ is_a: UBERON:0000478 ! extraembryonic structure relationship: RO:0002176 UBERON:0000922 ! connects embryo relationship: RO:0002176 UBERON:0001987 ! connects placenta relationship: RO:0002202 UBERON:0007806 ! develops from connecting stalk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192374,9 +192545,9 @@ relationship: part_of UBERON:0008886 ! pulmonary vascular system relationship: RO:0002150 UBERON:0000948 ! continuous with heart relationship: RO:0002150 UBERON:0002080 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! continuous with heart right ventricle relationship: RO:0002170 UBERON:0002080 ! connected to heart right ventricle -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192481,8 +192652,8 @@ relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tr relationship: has_part CL:0002332 ! ciliated cell of the bronchus relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: part_of UBERON:0002183 ! lobar bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0002341 @@ -192514,8 +192685,8 @@ relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: has_part CL:1000143 ! lung goblet cell relationship: has_part CL:1000223 ! lung neuroendocrine cell relationship: part_of UBERON:0002184 ! segmental bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0002342 @@ -192556,8 +192727,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002343 @@ -192623,7 +192794,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -192666,7 +192837,7 @@ is_a: UBERON:0015008 ! thoracic vertebra endochondral element intersection_of: UBERON:0015008 ! thoracic vertebra endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: RO:0002202 UBERON:0013507 ! develops from thoracic vertebra cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192745,7 +192916,7 @@ intersection_of: RO:0002473 UBERON:0001133 ! composed primarily of cardiac muscl relationship: has_part UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001133 ! composed primarily of cardiac muscle tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg" xsd:anyURI [Term] id: UBERON:0002350 @@ -192828,8 +192999,8 @@ relationship: capable_of_part_of GO:0060048 ! cardiac muscle contraction relationship: part_of UBERON:0002350 {source="ZFA"} ! conducting system of heart relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192876,8 +193047,8 @@ relationship: part_of UBERON:0002350 ! conducting system of heart relationship: RO:0002170 UBERON:0002085 ! connected to interatrial septum relationship: RO:0002170 UBERON:0005979 ! connected to crista terminalis relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192913,8 +193084,8 @@ is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle relationship: has_part CL:1000410 {source="FMA"} ! myocyte of atrioventricular node relationship: part_of UBERON:0004146 {source="GO"} ! His-Purkinje system relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192944,7 +193115,7 @@ is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle relationship: has_part CL:0002068 {source="FMA"} ! Purkinje myocyte relationship: part_of UBERON:8000009 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! Purkinje fiber network relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI [Term] id: UBERON:0002355 @@ -193027,7 +193198,7 @@ intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0035820 ! peritoneal sac relationship: part_of UBERON:0003697 {source="MP"} ! abdominal wall relationship: part_of UBERON:0035820 ! peritoneal sac -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI property_value: IAO:0000116 "TODO - in ZFA is_a epithelium" xsd:string [Term] @@ -193084,7 +193255,7 @@ is_a: UBERON:0000094 {source="FMA"} ! membrane organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010743 ! meningeal cluster relationship: RO:0002495 UBERON:0007645 {source="Bgee:AN"} ! immediate transformation of future meninx -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg" xsd:anyURI [Term] id: UBERON:0002361 @@ -193124,8 +193295,8 @@ xref: Wikipedia:Pia_mater is_a: UBERON:0000391 ! leptomeninx relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png" xsd:anyURI property_value: IAO:0000116 "consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system" xsd:string [Term] @@ -193156,7 +193327,7 @@ xref: Wikipedia:Arachnoid_mater is_a: UBERON:0000391 ! leptomeninx relationship: RO:0002160 NCBITaxon:40674 {source="ISBN:0073040584"} ! only in taxon Mammalia relationship: RO:0002473 GO:0071953 ! composed primarily of elastic fiber -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png" xsd:anyURI [Term] id: UBERON:0002363 @@ -193185,7 +193356,7 @@ xref: Wikipedia:Dura_mater is_a: UBERON:0002360 ! meninx relationship: RO:0002150 UBERON:0001773 {source="PMID:16496288"} ! continuous with sclera relationship: RO:0002495 UBERON:0007647 ! immediate transformation of ectomeninx -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:32443 {source="ISBN:0073040584"} [Term] @@ -193293,8 +193464,8 @@ is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0010147 ! male accessory sex gland relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia relationship: RO:0002202 UBERON:0003820 ! develops from prostate bud -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI property_value: IAO:0000116 "TODO - FMA treats the gland as part of the prostate - see also FMA:74119." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -193328,7 +193499,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0000949 ! endocrine system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI [Term] id: UBERON:0002369 @@ -193373,8 +193544,8 @@ is_a: UBERON:0006858 ! adrenal/interrenal gland is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000949 {source="FMA-abduced-lr"} ! endocrine system relationship: RO:0002254 UBERON:0000926 {source="Wikipedia"} ! has developmental contribution from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI [Term] id: UBERON:0002370 @@ -193423,10 +193594,10 @@ relationship: has_part UBERON:0003846 ! thymus epithelium relationship: part_of UBERON:0000153 ! anterior region of body relationship: RO:0002160 NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! only in taxon Gnathostomata relationship: RO:0002202 UBERON:0005562 {source="ZFA"} ! develops from thymus primordium -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Thymus.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg" xsd:anyURI property_value: IAO:0000116 "check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -193473,7 +193644,7 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -193484,7 +193655,6 @@ name: tonsil namespace: uberon def: "Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx." [MGI:cwg, MP:0002380] subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim synonym: "Mandel" RELATED [BTO:0001387] @@ -193508,7 +193678,6 @@ is_a: UBERON:0001962 ! gut-associated lymphoid tissue relationship: part_of UBERON:0001735 {source="cjm"} ! tonsillar ring relationship: RO:0001025 UBERON:0000167 ! located in oral cavity relationship: RO:0002433 UBERON:0001735 ! contributes to morphology of tonsillar ring -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002374 @@ -193538,7 +193707,7 @@ intersection_of: part_of UBERON:0004453 ! metacarpus region relationship: part_of UBERON:0010544 ! metacarpus skeleton relationship: RO:0002170 UBERON:0001435 ! connected to carpal bone relationship: RO:0002170 UBERON:0001436 ! connected to phalanx of manus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI [Term] id: UBERON:0002376 @@ -193667,7 +193836,7 @@ relationship: RO:0002373 UBERON:0002497 ! has muscle insertion acromion relationship: RO:0002373 UBERON:0007173 ! has muscle insertion lateral border of scapula relationship: RO:0002568 UBERON:0001112 {source="dbpedia"} ! has muscle antagonist latissimus dorsi muscle relationship: RO:0002568 UBERON:0001125 {source="dbpedia"} ! has muscle antagonist serratus ventralis -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -193699,7 +193868,7 @@ relationship: RO:0002005 UBERON:0003726 ! innervated_by thoracic nerve relationship: RO:0002372 UBERON:0000975 ! has muscle origin sternum relationship: RO:0002372 UBERON:0001105 ! has muscle origin clavicle bone relationship: RO:0002373 UBERON:0000976 ! has muscle insertion humerus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -193828,8 +193997,8 @@ intersection_of: UBERON:0002471 ! zeugopod intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0001460 {source="MA"} ! arm relationship: RO:0002551 UBERON:0010703 ! has skeleton forelimb zeugopod skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/50/Forearm_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/50/Forearm_labeled.png" xsd:anyURI [Term] id: UBERON:0002387 @@ -193874,7 +194043,7 @@ intersection_of: UBERON:0002470 ! autopod region intersection_of: part_of UBERON:0002103 ! hindlimb relationship: RO:0002202 UBERON:0006871 ! develops from embryonic footplate relationship: RO:0002551 UBERON:0001445 ! has skeleton skeleton of pes -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg" xsd:anyURI [Term] id: UBERON:0002389 @@ -193993,7 +194162,7 @@ is_a: BFO:0000002 is_a: UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0006558 ! lymphatic part of lymphoid system relationship: RO:0002494 UBERON:0000913 ! transformation of interstitial fluid -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png" xsd:anyURI [Term] id: UBERON:0002392 @@ -194031,7 +194200,7 @@ relationship: RO:0002176 UBERON:0001351 ! connects lacrimal sac relationship: RO:0002176 UBERON:0001707 ! connects nasal cavity relationship: RO:0002202 UBERON:0006266 ! develops from nasolacrimal groove relationship: RO:0002433 UBERON:0001750 ! contributes to morphology of lacrimal apparatus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI [Term] id: UBERON:0002394 @@ -194070,7 +194239,7 @@ relationship: channel_for UBERON:0001970 ! bile relationship: part_of UBERON:0001173 {source="EMAPA", source="MA"} ! biliary tree relationship: RO:0002202 UBERON:0008835 {source="XAO"} ! develops from hepatic diverticulum relationship: RO:0002433 UBERON:0001173 ! contributes to morphology of biliary tree -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI [Term] id: UBERON:0002396 @@ -194099,7 +194268,7 @@ relationship: part_of UBERON:0011085 ! palatoquadrate arch relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone relationship: RO:0002433 UBERON:0011156 ! contributes to morphology of facial skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -194143,7 +194312,7 @@ intersection_of: UBERON:0002470 ! autopod region intersection_of: part_of UBERON:0002102 ! forelimb relationship: RO:0002202 UBERON:0006875 ! develops from embryonic handplate relationship: RO:0002551 UBERON:0001442 ! has skeleton skeleton of manus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg" xsd:anyURI [Term] id: UBERON:0002400 @@ -194238,7 +194407,7 @@ relationship: adjacent_to UBERON:0002400 ! parietal pleura relationship: adjacent_to UBERON:0002401 ! visceral pleura relationship: RO:0002202 UBERON:0003887 {source="Wikipedia"} ! develops from intraembryonic coelom relationship: RO:0002572 UBERON:0009778 ! luminal space of pleural sac -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI [Term] id: UBERON:0002405 @@ -194295,7 +194464,7 @@ relationship: has_part UBERON:0001074 ! pericardial cavity relationship: has_part UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002407 ! pericardium relationship: RO:0002219 UBERON:0002359 {source="FMA"} ! surrounded by fibrous pericardium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI [Term] id: UBERON:0002407 @@ -194334,7 +194503,7 @@ relationship: has_part UBERON:0002359 ! fibrous pericardium relationship: has_part UBERON:0002406 ! pericardial sac relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002221 UBERON:0002349 ! surrounds myocardium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -194364,7 +194533,7 @@ intersection_of: UBERON:0022351 ! parietal serous membrane intersection_of: part_of UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002357 ! serous pericardium relationship: RO:0002371 UBERON:0006670 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! attached to central tendon of diaphragm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI [Term] id: UBERON:0002409 @@ -194424,7 +194593,7 @@ is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000010 {source="EMAPA", source="MA", source="NIFSTD", source="ZFA-modified-from-isa"} ! peripheral nervous system relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI [Term] id: UBERON:0002411 @@ -194455,7 +194624,7 @@ relationship: part_of UBERON:0000997 {source="MA"} ! mammalian vulva relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia relationship: RO:0002202 UBERON:0005876 {source="EHDAA2", source="Wikipedia"} ! develops from undifferentiated genital tubercle relationship: RO:0002433 UBERON:0005056 ! contributes to morphology of external female genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg" xsd:anyURI [Term] id: UBERON:0002412 @@ -194520,7 +194689,7 @@ is_a: UBERON:0015007 ! cervical vertebra endochondral element intersection_of: UBERON:0015007 ! cervical vertebra endochondral element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: RO:0002202 UBERON:0013505 ! develops from cervical vertebra cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -194577,7 +194746,7 @@ xref: EHDAA2_RETIRED:0003154 xref: EHDAA:6520 xref: EMAPA:17524 xref: EV:0100151 -xref: FBbt:00004969 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004969 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:72979 xref: galen:Surface xref: HAO:0000421 @@ -194666,7 +194835,7 @@ relationship: has_part CHEBI:18085 relationship: has_part CL:0000138 ! chondrocyte relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI [Term] id: UBERON:0002419 @@ -194711,7 +194880,7 @@ xref: SCTID:244434001 is_a: UBERON:0003528 ! brain gray matter is_a: UBERON:0007245 {source="FMA"} ! nuclear complex of neuraxis relationship: part_of UBERON:0010011 ! collection of basal ganglia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg" xsd:anyURI property_value: IAO:0000116 "it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done." xsd:string [Term] @@ -194805,9 +194974,9 @@ intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain relationship: RO:0002202 UBERON:0013149 {source="EHDAA2"} ! develops from hindbrain vesicle relationship: RO:0002433 UBERON:0002028 ! contributes to morphology of hindbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -194995,7 +195164,7 @@ is_a: UBERON:0000029 ! lymph node intersection_of: UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg" xsd:anyURI [Term] id: UBERON:0002435 @@ -195041,7 +195210,7 @@ relationship: part_of UBERON:0000204 {source="GO"} ! ventral part of telencephal relationship: part_of UBERON:0000369 {source="BTO"} ! corpus striatum relationship: part_of UBERON:0006098 {source="NIFSTD"} ! basal nuclear complex relationship: RO:0002433 UBERON:0010011 ! contributes to morphology of collection of basal ganglia -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI [Term] id: UBERON:0002437 @@ -195183,7 +195352,7 @@ intersection_of: RO:0002170 UBERON:0000981 ! connected to femur relationship: adjacent_to UBERON:0001485 ! knee joint relationship: part_of UBERON:0001465 ! knee relationship: RO:0002170 UBERON:0000981 ! connected to femur -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -195221,7 +195390,7 @@ is_a: UBERON:0000478 {source="FMA"} ! extraembryonic structure relationship: part_of UBERON:0001987 ! placenta relationship: RO:0002202 UBERON:0000459 ! develops from uterine wall relationship: RO:0002433 UBERON:0001987 ! contributes to morphology of placenta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png" xsd:anyURI property_value: IAO:0000116 "TODO - check mp syn" xsd:string [Term] @@ -195255,7 +195424,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0012276 ! endometrium glandular epithelium relationship: RO:0000086 PATO:0002299 {source="Wikipedia:Tubular_gland"} ! has quality tubular -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -195284,7 +195453,7 @@ is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0001533 ! subclavian artery relationship: RO:0002178 UBERON:0000310 ! supplies breast relationship: RO:0002252 UBERON:0001533 ! connecting branch of subclavian artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -195351,7 +195520,7 @@ intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0001255 ! drains urinary bladder relationship: RO:0002179 UBERON:0001255 ! drains urinary bladder relationship: RO:0002376 UBERON:0001317 ! tributary of internal iliac vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -195409,7 +195578,7 @@ is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system relationship: part_of UBERON:0002405 ! immune system relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI [Term] id: UBERON:0002466 @@ -195601,7 +195770,7 @@ relationship: part_of UBERON:0001677 ! sphenoid bone relationship: RO:0002202 UBERON:0005687 ! develops from orbitosphenoid cartilage element relationship: RO:0002202 UBERON:0009638 ! develops from orbitosphenoid ossification center relationship: RO:0002433 UBERON:0001677 ! contributes to morphology of sphenoid bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI [Term] id: UBERON:0002479 @@ -195723,7 +195892,7 @@ intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland relationship: RO:0002202 UBERON:0003820 {source="PMID:18977204"} ! develops from prostate bud relationship: RO:0002433 UBERON:0002367 ! contributes to morphology of prostate gland -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI [Term] id: UBERON:0002490 @@ -195748,8 +195917,8 @@ is_a: UBERON:0003685 ! cranial suture intersection_of: UBERON:0003685 ! cranial suture intersection_of: RO:0002176 UBERON:0000209 {cardinality="2"} ! connects tetrapod frontal bone relationship: RO:0002176 UBERON:0000209 ! connects tetrapod frontal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray134.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d1/Frontal_suture.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray134.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d1/Frontal_suture.png" xsd:anyURI [Term] id: UBERON:0002495 @@ -195797,7 +195966,7 @@ xref: VSAO:0005067 xref: Wikipedia:Acromion is_a: UBERON:0004530 ! bony projection relationship: part_of UBERON:0006849 ! scapula -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/79/Gray206.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/79/Gray206.png" xsd:anyURI [Term] id: UBERON:0002498 @@ -195828,7 +195997,7 @@ is_a: UBERON:0005813 ! tubercle is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0004652 ! humerus diaphysis relationship: RO:0002433 UBERON:0000976 ! contributes to morphology of humerus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png" xsd:anyURI [Term] id: UBERON:0002499 @@ -195848,7 +196017,7 @@ is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001849 {source="FMA"} ! membranous labyrinth relationship: RO:0001025 UBERON:0001844 ! located in cochlea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI property_value: IAO:0000116 "we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear" xsd:string [Term] @@ -195917,8 +196086,8 @@ is_a: UBERON:0015860 {source="FMA"} ! visceral abdominal lymph node intersection_of: UBERON:0002507 ! abdominal lymph node intersection_of: part_of UBERON:0002095 ! mesentery relationship: part_of UBERON:0002095 ! mesentery -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -195977,7 +196146,7 @@ relationship: has_part CL:0000175 ! luteal cell relationship: part_of UBERON:0000992 {source="MA"} ! ovary relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0001305 ! develops from ovarian follicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:7762 {source="PMID:20959416"} property_value: RO:0002175 NCBITaxon:9606 @@ -196006,7 +196175,7 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: RO:0002202 UBERON:0005863 ! develops from cartilaginous condensation relationship: RO:0002202 UBERON:0007844 {source="VSAO"} ! develops from cartilage element relationship: RO:0002285 UBERON:0002418 ! developmentally replaces cartilage tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI property_value: IAO:0000116 "placement in this class to be inferred" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern" xsd:anyURI @@ -196046,7 +196215,7 @@ xref: Wikipedia:Periosteum is_a: UBERON:0000158 ! membranous layer relationship: part_of UBERON:0001474 ! bone element relationship: RO:0002473 UBERON:0011822 ! composed primarily of dense irregular connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Bone_growth.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Bone_growth.png" xsd:anyURI [Term] id: UBERON:0002517 @@ -196072,7 +196241,7 @@ is_a: UBERON:0000075 ! subdivision of skeletal system relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0002241 ! chondrocranium relationship: RO:0002433 UBERON:0003128 ! contributes to morphology of cranium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI [Term] id: UBERON:0002518 @@ -196100,7 +196269,7 @@ is_a: UBERON:0006585 ! vestibular organ relationship: capable_of_part_of GO:0060007 ! linear vestibuloocular reflex relationship: part_of UBERON:0001862 ! vestibular labyrinth relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI property_value: IAO:0000116 "Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia" xsd:string [Term] @@ -196124,7 +196293,7 @@ intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 GO:0071953 ! composed primarily of elastic fiber relationship: RO:0000086 PATO:0001171 ! has quality elastic relationship: RO:0002473 GO:0071953 ! composed primarily of elastic fiber -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png" xsd:anyURI [Term] id: UBERON:0002522 @@ -196148,7 +196317,7 @@ is_a: UBERON:0004797 {source="MA"} ! blood vessel layer relationship: has_part UBERON:0002521 {source="cjm"} ! elastic tissue relationship: has_part UBERON:0004237 {source="cjm"} ! blood vessel smooth muscle relationship: RO:0002219 UBERON:0005734 ! surrounded by tunica adventitia of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI [Term] id: UBERON:0002523 @@ -196175,7 +196344,7 @@ is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: adjacent_to UBERON:0010161 {source="ISBN:0073040584"} ! lumen of blood vessel relationship: has_part UBERON:0001986 ! endothelium relationship: RO:0002219 UBERON:0002522 ! surrounded by tunica media -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI property_value: IAO:0000116 "the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure" xsd:string property_value: IAO:0000116 "the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts" xsd:string @@ -196243,7 +196412,7 @@ xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 xref: EMAPA:18425 -xref: FBbt:00100317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7146 xref: FMA:86294 xref: galen:Gland @@ -196260,7 +196429,7 @@ is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: produces UBERON:0000463 ! organism substance relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] id: UBERON:0002532 @@ -196284,7 +196453,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -196326,7 +196495,7 @@ subset: uberon_slim synonym: "sensillum" EXACT [FBbt:00007152, HAO:0000933] xref: BTO:0001237 xref: EFO:0000939 -xref: FBbt:00007152 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007152 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000933 xref: MAT:0000163 xref: MIAA:0000163 @@ -196399,7 +196568,7 @@ relationship: part_of UBERON:0008814 ! pharyngeal arch system relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0007690 {source="PMID:16313389"} ! developmentally induced by early pharyngeal endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI [Term] id: UBERON:0002540 @@ -196508,7 +196677,7 @@ synonym: "wriggler" NARROW [Wikipedia:Larva] synonym: "zoea" NARROW [Wikipedia:Larva] xref: AEO:0000126 xref: BTO:0000707 -xref: FBbt:00001727 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001727 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000459 xref: TAO:0002048 xref: Wikipedia:Larva @@ -196637,7 +196806,7 @@ xref: SCTID:279215006 xref: UMLS:C0458337 {source="BIRNLEX:1128"} xref: Wikipedia:Limbic_lobe is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Human_brain_inferior-medial_view_description.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Human_brain_inferior-medial_view_description.JPG" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -196661,7 +196830,7 @@ xref: UMLS:C0152411 {source="ncithesaurus:Cochlear_Nuclei", source="BIRNLEX:1151 xref: Wikipedia:Cochlear_nuclei is_a: UBERON:0019263 ! gray matter of hindbrain relationship: part_of UBERON:0001896 ! medulla oblongata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI [Term] id: UBERON:0002616 @@ -196824,7 +196993,7 @@ xref: neuronames:351 {source="BIRNLEX:1461"} xref: SCTID:361550004 xref: Wikipedia:Metathalamus is_a: UBERON:0015233 ! nucleus of dorsal thalamus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/ThalamicNuclei.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/ThalamicNuclei.png" xsd:anyURI [Term] id: UBERON:0002707 @@ -196865,7 +197034,7 @@ xref: Wikipedia:Corticospinal_tract is_a: UBERON:0001018 ! axon tract relationship: part_of UBERON:0025525 ! motor system relationship: part_of UBERON:0036224 ! corticobulbar and corticospinal tracts -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ac/Gray684.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ac/Gray684.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -196941,7 +197110,7 @@ xref: PBA:128012976 xref: Wikipedia:Basal_forebrain is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001890 {source="BTO"} ! forebrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Basal_Forebrain_Monakhos_2007.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Basal_Forebrain_Monakhos_2007.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -197110,8 +197279,8 @@ is_a: UBERON:0001869 ! cerebral hemisphere intersection_of: UBERON:0001869 ! cerebral hemisphere intersection_of: BSPO:0000120 UBERON:0000955 ! brain relationship: BSPO:0000120 UBERON:0000955 ! brain -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0002813 @@ -197128,8 +197297,8 @@ is_a: UBERON:0001869 ! cerebral hemisphere intersection_of: UBERON:0001869 ! cerebral hemisphere intersection_of: BSPO:0000121 UBERON:0000955 ! brain relationship: BSPO:0000121 UBERON:0000955 ! brain -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0002827 @@ -197207,7 +197376,7 @@ xref: UMLS:C0175500 {source="BIRNLEX:2567"} xref: Wikipedia:Ventral_cochlear_nucleus is_a: UBERON:0001720 ! cochlear nucleus disjoint_from: UBERON:0002829 {source="lexical"} ! dorsal cochlear nucleus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI [Term] id: UBERON:0002829 @@ -197240,7 +197409,7 @@ xref: UMLS:C0175499 {source="BIRNLEX:2569", source="ncithesaurus:Dorsal_Cochlear xref: UMLS:C1281210 {source="BIRNLEX:2569"} xref: Wikipedia:Dorsal_cochlear_nucleus is_a: UBERON:0001720 ! cochlear nucleus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI [Term] id: UBERON:0002830 @@ -197369,7 +197538,7 @@ is_a: UBERON:0007635 ! nucleus of medulla oblongata intersection_of: UBERON:0000126 ! cranial nerve nucleus intersection_of: extends_fibers_into UBERON:0001650 ! hypoglossal nerve relationship: extends_fibers_into UBERON:0001650 ! hypoglossal nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI [Term] id: UBERON:0002893 @@ -197468,8 +197637,8 @@ intersection_of: RO:0002176 UBERON:0001872 ! connects parietal lobe relationship: part_of UBERON:0000956 {source="NIFSTD"} ! cerebral cortex relationship: RO:0002176 UBERON:0001870 ! connects frontal cortex relationship: RO:0002176 UBERON:0001872 ! connects parietal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray726_central_sulcus.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/b6/Central_sulcus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray726_central_sulcus.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/b6/Central_sulcus.png" xsd:anyURI [Term] id: UBERON:0002921 @@ -197503,7 +197672,7 @@ xref: SCTID:369225004 xref: UMLS:C0228186 {source="BIRNLEX:4041", source="ncithesaurus:Longitudinal_Fissure"} xref: Wikipedia:Medial_longitudinal_fissure is_a: UBERON:0014466 {source="FMA"} ! subarachnoid fissure -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI [Term] id: UBERON:0002925 @@ -197707,9 +197876,9 @@ relationship: has_part UBERON:0002128 ! superior olivary complex relationship: has_part UBERON:0002148 ! locus ceruleus relationship: has_part UBERON:0002149 ! superior salivatory nucleus relationship: part_of UBERON:0000988 ! pons -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -197751,7 +197920,7 @@ is_a: UBERON:0005844 ! spinal cord segment intersection_of: UBERON:0005844 ! spinal cord segment intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0008231 ! dorsal thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -197839,7 +198008,7 @@ intersection_of: RO:0002387 UBERON:0001846 ! has potential to develop into inter relationship: part_of UBERON:0000924 ! ectoderm relationship: RO:0002202 UBERON:0006273 ! develops from otic pit relationship: RO:0002387 UBERON:0001846 ! has potential to develop into internal ear -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png" xsd:anyURI [Term] id: UBERON:0003052 @@ -198077,7 +198246,7 @@ relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme relationship: RO:0002202 UBERON:0000926 {source="XAO"} ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003066 @@ -198113,7 +198282,7 @@ xref: Wikipedia:Second_pharyngeal_arch xref: XAO:0000098 xref: ZFA:0001611 is_a: UBERON:0002539 ! pharyngeal arch -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI [Term] id: UBERON:0003067 @@ -198149,7 +198318,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003069 @@ -198297,7 +198466,7 @@ intersection_of: RO:0002387 UBERON:0000965 ! has potential to develop into lens relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye relationship: RO:0002256 UBERON:0004128 ! developmentally induced by optic vesicle relationship: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003074 @@ -198328,7 +198497,7 @@ is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct relationship: RO:0002202 UBERON:0003060 ! develops from pronephric duct relationship: RO:0002202 UBERON:0005792 {source="EHDAA2"} ! develops from nephric ridge -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI property_value: IAO:0000116 "Consider adding subclasses for male and female specific variants" xsd:string property_value: IAO:0000116 "TODO - mesonephric portion of the nephric duct" xsd:string @@ -198365,7 +198534,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003076 @@ -198412,7 +198581,7 @@ is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000922 ! embryo relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003078 @@ -198482,7 +198651,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003082 @@ -198520,7 +198689,7 @@ is_a: BFO:0000002 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome relationship: RO:0002433 UBERON:0001630 ! contributes to morphology of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI property_value: IAO:0000116 "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string [Term] @@ -198618,7 +198787,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003091 @@ -198670,7 +198839,7 @@ is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034705 {source="EHDAA2"} ! developing neuroepithelium relationship: part_of UBERON:0001894 ! diencephalon relationship: RO:0002202 UBERON:0003072 ! develops from optic cup -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003099 @@ -198714,7 +198883,7 @@ synonym: "female human body" NARROW SENSU [FMA:67812] xref: AAO:0010030 xref: BILA:0000028 xref: CARO:0000028 -xref: FBbt:00007011 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67812 xref: HAO:0000028 xref: SCTID:362608006 @@ -198737,7 +198906,7 @@ synonym: "male human body" NARROW SENSU [FMA:67811] xref: AAO:0010033 xref: BILA:0000027 xref: CARO:0000027 -xref: FBbt:00007004 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007004 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67811 xref: HAO:0000027 xref: SCTID:362609003 @@ -198826,7 +198995,7 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002254 UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! has developmental contribution from mesoderm relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -199230,7 +199399,7 @@ relationship: has_part UBERON:0003265 ! chorionic mesenchyme relationship: has_part UBERON:0003374 ! chorionic ectoderm relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota relationship: RO:0002202 UBERON:0005971 {source="ISBN:0073040584"} ! develops from amniotic fold -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -199273,10 +199442,10 @@ relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -199471,7 +199640,7 @@ synonym: "organ of gustatory system" EXACT [OBOL:automatic] synonym: "organ of taste system" EXACT [OBOL:automatic] synonym: "taste organ" EXACT [] synonym: "taste system organ" EXACT [OBOL:automatic] -xref: FBbt:00005159 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005159 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:77853 is_a: UBERON:0000005 ! chemosensory organ intersection_of: UBERON:0000062 ! organ @@ -199955,7 +200124,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0014477 ! thoracic skeleton relationship: part_of UBERON:0014478 ! rib skeletal system relationship: RO:0002433 UBERON:0005944 ! contributes to morphology of axial skeleton plus cranial skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png" xsd:anyURI [Term] id: UBERON:0003253 @@ -199973,7 +200142,7 @@ is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0002228 ! rib relationship: part_of UBERON:0010388 {source="PMID:15906248"} ! proximal segment of rib -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png" xsd:anyURI [Term] id: UBERON:0003254 @@ -201779,8 +201948,8 @@ is_a: UBERON:0002183 ! lobar bronchus intersection_of: UBERON:0002183 ! lobar bronchus intersection_of: part_of UBERON:0002167 ! right lung relationship: part_of UBERON:0006518 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! right lung lobe -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0003405 @@ -201799,8 +201968,8 @@ is_a: UBERON:0002183 ! lobar bronchus intersection_of: UBERON:0002183 ! lobar bronchus intersection_of: part_of UBERON:0002168 ! left lung relationship: part_of UBERON:0008951 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! left lung lobe -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0003406 @@ -202754,7 +202923,7 @@ is_a: UBERON:0003496 ! head blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0002037 ! supplies cerebellum relationship: RO:0002178 UBERON:0002037 ! supplies cerebellum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg" xsd:anyURI [Term] id: UBERON:0003473 @@ -202856,7 +203025,7 @@ is_a: UBERON:0013136 ! vein of lip intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0001835 ! drains lower lip relationship: RO:0002179 UBERON:0001835 ! drains lower lip -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -203679,8 +203848,8 @@ name: hindlimb skin namespace: uberon def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "lower limb skin" EXACT [FMA:23102] +synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -205063,9 +205232,9 @@ intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea relationship: RO:0002202 UBERON:0007267 ! develops from trachea pre-cartilage rings -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI property_value: IAO:0000116 "check whether to classify as part of splanchoncranium" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -205728,7 +205897,7 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000916 ! luminal space of abdomen relationship: part_of UBERON:0035819 ! abdominopelvic cavity relationship: RO:0002572 UBERON:0000916 ! luminal space of abdomen -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0003685 @@ -205780,7 +205949,7 @@ intersection_of: UBERON:0013685 ! foramen of skull intersection_of: RO:0002570 UBERON:0001896 ! conduit for medulla oblongata relationship: RO:0001025 UBERON:0001676 ! located in occipital bone relationship: RO:0002570 UBERON:0001896 ! conduit for medulla oblongata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png" xsd:anyURI [Term] id: UBERON:0003688 @@ -205845,7 +206014,7 @@ intersection_of: RO:0002176 UBERON:0001105 ! connects clavicle bone intersection_of: RO:0002176 UBERON:0002497 ! connects acromion relationship: RO:0002176 UBERON:0001105 ! connects clavicle bone relationship: RO:0002176 UBERON:0002497 ! connects acromion -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png" xsd:anyURI [Term] id: UBERON:0003694 @@ -205874,7 +206043,7 @@ intersection_of: RO:0002176 UBERON:0001093 ! connects vertebral bone 2 relationship: part_of UBERON:0011138 ! postcranial axial skeletal system relationship: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 relationship: RO:0002176 UBERON:0001093 ! connects vertebral bone 2 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI [Term] id: UBERON:0003695 @@ -205908,7 +206077,7 @@ intersection_of: RO:0002176 UBERON:0002374 ! connects metacarpal bone relationship: part_of UBERON:0002389 ! manual digit relationship: RO:0002176 UBERON:0002234 ! connects proximal phalanx of manus relationship: RO:0002176 UBERON:0002374 ! connects metacarpal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png" xsd:anyURI property_value: IAO:0000116 "we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part" xsd:string [Term] @@ -205939,7 +206108,7 @@ intersection_of: RO:0002176 UBERON:0003867 ! connects distal phalanx of pes relationship: part_of UBERON:0001466 ! pedal digit relationship: RO:0002176 UBERON:0001448 ! connects metatarsal bone relationship: RO:0002176 UBERON:0003867 ! connects distal phalanx of pes -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png" xsd:anyURI property_value: IAO:0000116 "we follow FMA in making these joints part of digits" xsd:string [Term] @@ -205967,7 +206136,7 @@ is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0003703 @@ -206036,7 +206205,7 @@ xref: Wikipedia:Circle_of_Willis is_a: UBERON:0004573 ! systemic artery relationship: overlaps UBERON:0007142 {source="FMA-modified"} ! left internal carotid artery relationship: overlaps UBERON:0007143 {source="FMA-modified"} ! right internal carotid artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI [Term] id: UBERON:0003711 @@ -206065,7 +206234,7 @@ xref: Wikipedia:Brachiocephalic_vein is_a: UBERON:0001638 ! vein relationship: part_of UBERON:0007204 ! brachiocephalic vasculature relationship: RO:0002170 UBERON:0001585 ! connected to anterior vena cava -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -206113,10 +206282,10 @@ xref: UMLS:C0038001 {source="ncithesaurus:Splenic_Vein"} xref: Wikipedia:Splenic_vein is_a: UBERON:0001638 ! vein relationship: RO:0002170 UBERON:0001639 ! connected to hepatic portal vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -206151,6 +206320,7 @@ id: UBERON:0003715 name: splanchnic nerve namespace: uberon def: "The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia." [MP:0008318] +subset: human_reference_atlas subset: pheno_slim synonym: "splanchnic nerves" RELATED [BAMS:spn] synonym: "visceral nerve" RELATED [Wikipedia:Splanchnic_nerves] @@ -206166,12 +206336,14 @@ intersection_of: UBERON:0001021 ! nerve intersection_of: RO:0002134 UBERON:0000916 ! innervates abdomen relationship: RO:0002134 UBERON:0000916 ! innervates abdomen relationship: RO:0002433 UBERON:0000013 ! contributes to morphology of sympathetic nervous system +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003716 name: recurrent laryngeal nerve namespace: uberon def: "A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch." [Wikipedia:Recurrent_laryngeal_nerve] +subset: human_reference_atlas synonym: "inferior laryngeal nerve" RELATED [GAID:804] synonym: "nervus laryngeus recurrens" EXACT OMO:0003011 [Wikipedia:Recurrent_laryngeal_nerve] synonym: "ramus recurrens" RELATED [AAO:0010754] @@ -206191,6 +206363,7 @@ is_a: UBERON:0035642 ! laryngeal nerve relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda relationship: RO:0002202 UBERON:0003117 {source="Wikipedia"} ! develops from pharyngeal arch 6 relationship: RO:0002380 UBERON:0001759 ! branching part of vagus nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003718 @@ -206215,6 +206388,7 @@ id: UBERON:0003721 name: lingual nerve namespace: uberon def: "The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue." [Wikipedia:Lingual_nerve] +subset: human_reference_atlas synonym: "lingual branch of trigeminal nerve" EXACT [] synonym: "trigeminal nerve lingual branch" EXACT [] synonym: "trigeminal V nerve lingual branch" EXACT [MA:0001102] @@ -206231,12 +206405,14 @@ intersection_of: UBERON:0001021 ! nerve intersection_of: RO:0002134 UBERON:0001723 ! innervates tongue relationship: RO:0002134 UBERON:0001723 ! innervates tongue relationship: RO:0002380 UBERON:0000375 ! branching part of mandibular nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003726 name: thoracic nerve namespace: uberon def: "The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls." [MESH:A08.800.800.720.800] +subset: human_reference_atlas synonym: "nervi thoracici" RELATED OMO:0003011 [Wikipedia:Thoracic_nerves] synonym: "nervus thoracis" EXACT OMO:0003011 [FMA:5860, FMA:TA] synonym: "pectoral nerve" RELATED [GAID:857] @@ -206251,6 +206427,7 @@ is_a: UBERON:0001780 ! spinal nerve intersection_of: UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0003038 ! thoracic spinal cord relationship: extends_fibers_into UBERON:0003038 ! thoracic spinal cord +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003727 @@ -206272,7 +206449,7 @@ xref: SCTID:279568001 xref: UMLS:C1285089 {source="ncithesaurus:Intercostal_Nerve"} xref: Wikipedia:Intercostal_nerves is_a: UBERON:0001780 ! spinal nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png" xsd:anyURI [Term] id: UBERON:0003728 @@ -206296,7 +206473,7 @@ xref: Wikipedia:Mediastinum is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0002224 ! thoracic cavity relationship: RO:0002219 UBERON:0035431 {source="FMA"} ! surrounded by mediastinal pleura -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png" xsd:anyURI [Term] id: UBERON:0003729 @@ -206922,7 +207099,7 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002371 UBERON:0000991 ! attached to gonad relationship: RO:0002371 UBERON:0000991 ! attached to gonad -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI [Term] id: UBERON:0003849 @@ -207151,7 +207328,7 @@ xref: ZFA:0001066 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0010358 ! arch of centrum of vertebra relationship: RO:0002202 UBERON:0006063 ! develops from cartilaginous neural arch -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI [Term] id: UBERON:0003864 @@ -207392,7 +207569,7 @@ relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia relationship: RO:0002176 UBERON:0000995 ! connects uterus relationship: RO:0002176 UBERON:0003984 ! connects uterine tube infundibulum relationship: RO:0002202 UBERON:0003890 ! develops from Mullerian duct -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -207425,7 +207602,7 @@ is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0003891 @@ -207650,7 +207827,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -207725,7 +207902,7 @@ intersection_of: RO:0002387 UBERON:0001264 ! has potential to develop into pancr relationship: part_of UBERON:0007026 ! presumptive gut relationship: RO:0002202 UBERON:0000925 {source="Wikipedia"} ! develops from endoderm relationship: RO:0002387 UBERON:0001264 ! has potential to develop into pancreas -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003922 @@ -207753,8 +207930,8 @@ relationship: RO:0002202 UBERON:0001041 {source="Wikipedia:Pancreas#Embryologica relationship: RO:0002202 UBERON:0001555 ! develops from digestive tract relationship: RO:0002202 UBERON:0002114 ! develops from duodenum relationship: RO:0002202 UBERON:0009497 {source="EHDAA2-inferred"} ! develops from epithelium of foregut-midgut junction -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003923 @@ -207785,7 +207962,7 @@ relationship: part_of UBERON:0010375 {source="EHDAA2"} ! pancreas dorsal primord relationship: RO:0002202 UBERON:0001045 {source="XAO"} ! develops from midgut relationship: RO:0002256 UBERON:0002328 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! developmentally induced by notochord relationship: RO:0002256 UBERON:0005805 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! developmentally induced by dorsal aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003924 @@ -207813,7 +207990,7 @@ xref: ZFA:0001369 is_a: UBERON:0003922 ! pancreatic epithelial bud relationship: part_of UBERON:0010376 {source="EHDAA2"} ! pancreas ventral primordium relationship: RO:0002202 UBERON:0008835 {source="PMID:16417468", source="WP"} ! develops from hepatic diverticulum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003928 @@ -207847,7 +208024,7 @@ synonym: "gut epithelium" EXACT [EHDAA2:0004567, MA:0003201, ZFA:0005123] xref: BTO:0000956 xref: EHDAA2:0004567 xref: EMAPA:32928 -xref: FBbt:00047166 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00047166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MA:0003201 xref: NCIT:C12963 xref: TAO:0005123 @@ -208051,7 +208228,7 @@ relationship: channels_from UBERON:0001343 ! seminiferous tubule of testis relationship: channels_into UBERON:0006946 ! efferent duct relationship: part_of UBERON:0005051 ! mediastinum testis relationship: RO:0002202 UBERON:0005297 {source="Wikipedia"} ! develops from testis sex cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI property_value: IAO:0000116 "add more specific classification e.g. anastomosing network - consider FMA:3726" xsd:string [Term] @@ -208119,8 +208296,8 @@ xref: FMA:67611 xref: galen:Valve is_a: UBERON:0000064 ! organ part relationship: capable_of GO:0065008 ! regulation of biological quality -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI [Term] id: UBERON:0003980 @@ -208173,7 +208350,7 @@ xref: AAO:0010250 xref: Wikipedia:Conus_arteriosus is_a: UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0002080 ! heart right ventricle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI [Term] id: UBERON:0003984 @@ -208194,7 +208371,7 @@ xref: Wikipedia:Infundibulum_of_uterine_tube is_a: UBERON:0013515 {source="FMA"} ! subdivision of oviduct relationship: part_of UBERON:0003889 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! fallopian tube relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:8782 property_value: RO:0002175 NCBITaxon:9606 @@ -208296,7 +208473,7 @@ xref: XAO:0000220 is_a: BFO:0000002 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png" xsd:anyURI [Term] id: UBERON:0004021 @@ -208419,7 +208596,7 @@ is_a: UBERON:0005292 ! extraembryonic tissue relationship: part_of UBERON:0003124 ! chorion membrane relationship: part_of UBERON:8600038 ! placental disc relationship: RO:0002433 UBERON:0003124 ! contributes to morphology of chorion membrane -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -208513,7 +208690,7 @@ xref: Wikipedia:Osseous_ampullae is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0001856 {source="MA"} ! semicircular duct -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg" xsd:anyURI property_value: IAO:0000116 "TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as 'ampulla of anterior semicircular canal'" xsd:string [Term] @@ -208532,7 +208709,7 @@ property_value: seeAlso UBERON:0004341 id: UBERON:0004053 name: external male genitalia namespace: uberon -def: "The external masculine genital organs, including the penis and scrotum." [MP:0009199] +def: "The external masculine genital organs." [MP:0009199] comment: TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 subset: organ_slim subset: pheno_slim @@ -208551,6 +208728,8 @@ intersection_of: part_of UBERON:0000079 ! male reproductive system disjoint_from: UBERON:0005056 ! external female genitalia disjoint_from: UBERON:0009196 ! indifferent external genitalia relationship: RO:0002433 UBERON:0000079 ! contributes to morphology of male reproductive system +property_value: RO:0002175 NCBITaxon:50557 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004054 @@ -208732,7 +208911,7 @@ xref: VHOG:0001319 xref: Wikipedia:Frontonasal_prominence is_a: UBERON:0009292 ! embryonic nasal process relationship: BSPO:0005001 UBERON:0000033 ! head -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png" xsd:anyURI [Term] id: UBERON:0004067 @@ -208755,7 +208934,7 @@ is_a: UBERON:0009292 ! embryonic nasal process disjoint_from: UBERON:0004068 {source="lexical"} ! medial nasal prominence relationship: part_of UBERON:0004066 {source="EHDAA2"} ! frontonasal prominence relationship: RO:0002202 UBERON:0004066 {source="Wikipedia"} ! develops from frontonasal prominence -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI [Term] id: UBERON:0004068 @@ -208780,7 +208959,7 @@ is_a: UBERON:0009292 ! embryonic nasal process relationship: BSPO:0000126 UBERON:0008816 ! embryonic head relationship: part_of UBERON:0004066 {source="EHDAA2"} ! frontonasal prominence relationship: RO:0002202 UBERON:0004066 {source="Wikipedia"} ! develops from frontonasal prominence -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png" xsd:anyURI [Term] id: UBERON:0004086 @@ -208831,10 +209010,10 @@ xref: UMLS:C0042460 {source="ncithesaurus:Vena_Cava"} xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] id: UBERON:0004088 @@ -208900,7 +209079,7 @@ xref: SCTID:279371005 xref: Wikipedia:Collecting_duct_system is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002113 ! kidney -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -209030,7 +209209,7 @@ relationship: RO:0002219 UBERON:0010063 ! surrounded by tympanic cavity epitheli relationship: RO:0002221 UBERON:0001686 ! surrounds auditory ossicle bone relationship: RO:0002285 UBERON:0005625 {source="EHDAA2"} ! developmentally replaces tubotympanic recess lumen relationship: RO:0002572 UBERON:0001756 ! luminal space of middle ear -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI [Term] id: UBERON:0004115 @@ -209299,7 +209478,7 @@ relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye relationship: RO:0002202 UBERON:0002346 {source="GO-def"} ! develops from neurectoderm relationship: RO:0002202 UBERON:0003071 {source="ZFA"} ! develops from eye primordium relationship: RO:0002256 UBERON:0004880 ! developmentally induced by chordamesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI [Term] id: UBERON:0004129 @@ -209530,8 +209709,8 @@ intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000948 ! heart intersection_of: RO:0002179 UBERON:0002349 ! drains myocardium relationship: RO:0002179 UBERON:0002349 ! drains myocardium -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0004151 @@ -209899,7 +210078,7 @@ is_a: UBERON:0007685 ! region of nephron tubule relationship: part_of UBERON:0003455 ! inner renal medulla loop of Henle relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle relationship: RO:0002433 UBERON:0005164 ! contributes to morphology of ascending limb of loop of Henle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "check relationship to distal tubule" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -209922,6 +210101,46 @@ def: "Short nephrons are associated with mid-cortical glomeruli, and have no sho xref: FMA:272051 is_a: UBERON:0001285 ! nephron +[Term] +id: UBERON:0004196 +name: proximal convoluted tubule segment 1 +namespace: uberon +alt_id: UBERON:0006432 +def: "The S1 portion is the initial portion of the proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO]." [GO:0072031, http://sourceforge.net/tracker/?func=detail&atid=440764&aid=3298740&group_id=36855] +subset: human_reference_atlas +synonym: "proximal tubule segment 1" EXACT [MA:0002612] +synonym: "S1" BROAD [GO:0072031] +synonym: "S1 portion of renal tubule" EXACT [] +synonym: "S1 portion of tubule" EXACT [] +synonym: "segment 1 of proximal tubule" EXACT [EMAPA:29657] +xref: EMAPA:29657 +xref: MA:0002612 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0006555 ! excretory tube +relationship: capable_of_part_of GO:0070295 {source="GO"} ! renal water absorption +relationship: part_of UBERON:0001287 {source="GO"} ! proximal convoluted tubule +property_value: RO:0002175 NCBITaxon:9606 + +[Term] +id: UBERON:0004197 +name: proximal convoluted tubule segment 2 +namespace: uberon +alt_id: UBERON:0006433 +def: "The S2 portion of the tubule is involved in reabsorption of water and sodium chloride[GO]." [GO:0072032] +subset: human_reference_atlas +synonym: "proximal tubule segment 2" EXACT [MA:0002613] +synonym: "S2" BROAD [GO:0072032] +synonym: "S2 portion of renal tubule" EXACT [] +synonym: "S2 portion of tubule" EXACT [] +synonym: "segment 2 of proximal tubule" EXACT [EMAPA:29659] +xref: EMAPA:29659 +xref: MA:0002613 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0006555 ! excretory tube +relationship: capable_of_part_of GO:0070295 {source="GO"} ! renal water absorption +relationship: part_of UBERON:0001287 {source="GO"} ! proximal convoluted tubule +property_value: RO:0002175 NCBITaxon:9606 + [Term] id: UBERON:0004198 name: comma-shaped body @@ -209984,11 +210203,11 @@ xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000362 ! renal medulla relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -210577,8 +210796,8 @@ is_a: UBERON:0004228 ! urinary bladder smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001258 ! neck of urinary bladder relationship: part_of UBERON:0001258 ! neck of urinary bladder -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI [Term] id: UBERON:0004231 @@ -210870,8 +211089,8 @@ intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002185 ! bronchus relationship: has_part CL:0002598 ! bronchial smooth muscle cell relationship: part_of UBERON:0002185 ! bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0004243 @@ -211630,13 +211849,14 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: adjacent_to UBERON:0002081 ! cardiac atrium relationship: adjacent_to UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0000948 ! heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png" xsd:anyURI [Term] id: UBERON:0004293 name: parasympathetic nerve namespace: uberon def: "A nerve that is part of a parasympathetic nervous system [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas synonym: "nerve of parasympathetic nervous system" EXACT [OBOL:automatic] xref: EHDAA2:0001401 xref: EMAPA:17271 @@ -211651,6 +211871,7 @@ relationship: extends_fibers_into UBERON:0001808 ! parasympathetic ganglion relationship: part_of UBERON:0000011 ! parasympathetic nervous system relationship: RO:0002254 UBERON:0005428 {source="NCBIBook:NBK10065"} ! has developmental contribution from vagal neural crest relationship: RO:0002254 UBERON:0010075 {source="NCBIBook:NBK10065"} ! has developmental contribution from sacral neural crest +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004294 @@ -211737,7 +211958,7 @@ intersection_of: UBERON:0003221 ! phalanx intersection_of: proximally_connected_to UBERON:0004301 ! middle phalanx relationship: part_of UBERON:0009551 ! distal segment of digit relationship: proximally_connected_to UBERON:0004301 ! middle phalanx -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg" xsd:anyURI [Term] id: UBERON:0004301 @@ -211805,7 +212026,7 @@ relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amnio relationship: RO:0002202 UBERON:0000162 {source="Hymans"} ! develops from cloaca relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm relationship: RO:0002254 UBERON:0004872 {source="ISBN:0073040584"} ! has developmental contribution from splanchnic layer of lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png" xsd:anyURI [Term] id: UBERON:0004341 @@ -211829,7 +212050,7 @@ is_a: UBERON:0005291 ! embryonic tissue relationship: RO:0002202 UBERON:0008780 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="ISBN:9780878932504"} ! develops from inner cell mass derived epiblast relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI [Term] id: UBERON:0004345 @@ -211915,7 +212136,7 @@ relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0004357 ! paired limb/fin bud relationship: produces PR:000007499 ! fibroblast growth factor 8 relationship: RO:0002256 UBERON:0003104 ! developmentally induced by mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg" xsd:anyURI [Term] id: UBERON:0004357 @@ -211969,7 +212190,7 @@ xref: Wikipedia:First_pharyngeal_arch xref: XAO:0000097 xref: ZFA:0001612 is_a: UBERON:0002539 ! pharyngeal arch -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI [Term] id: UBERON:0004363 @@ -212015,7 +212236,7 @@ relationship: part_of UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0007303 {source="ZFA"} ! pharyngeal vasculature relationship: RO:0002387 UBERON:0001637 ! has potential to develop into artery relationship: RO:0002433 UBERON:0002539 ! contributes to morphology of pharyngeal arch -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png" xsd:anyURI property_value: IAO:0000116 "add specific artery derivatives" xsd:string [Term] @@ -212356,7 +212577,7 @@ is_a: UBERON:0004380 ! proximal epiphysis is_a: UBERON:0004382 ! epiphysis of humerus intersection_of: UBERON:0004380 ! proximal epiphysis intersection_of: part_of UBERON:0000976 ! humerus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png" xsd:anyURI [Term] id: UBERON:0004412 @@ -212529,8 +212750,8 @@ relationship: distally_connected_to UBERON:0004453 ! metacarpus region relationship: part_of UBERON:0002398 ! manus relationship: proximally_connected_to UBERON:0002386 ! forelimb zeugopod relationship: RO:0002551 UBERON:0009880 ! has skeleton carpal skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cc/Hand_parts.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cc/Hand_parts.jpg" xsd:anyURI [Term] id: UBERON:0004453 @@ -212556,7 +212777,7 @@ intersection_of: UBERON:0009877 ! metapodium region intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0012141 {source="PHENOSCAPE:ni"} ! manual digitopodium region relationship: RO:0002551 UBERON:0010544 ! has skeleton metacarpus skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI property_value: IAO:0000116 "Note that along with FMA we treat this as a limb segment rather than a purely skeletal element" xsd:string [Term] @@ -212593,7 +212814,7 @@ relationship: distally_connected_to UBERON:0000983 ! metatarsus region relationship: part_of UBERON:0002387 ! pes relationship: proximally_connected_to UBERON:0003823 ! hindlimb zeugopod relationship: RO:0002551 UBERON:0009879 ! has skeleton tarsal skeleton -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI [Term] id: UBERON:0004455 @@ -213167,8 +213388,8 @@ intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002187 ! terminal bronchiole relationship: has_part CL:4033017 ! bronchiolar smooth muscle cell relationship: part_of UBERON:0002187 ! terminal bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0004517 @@ -213182,8 +213403,8 @@ intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002188 ! respiratory bronchiole relationship: has_part CL:4033017 ! bronchiolar smooth muscle cell relationship: part_of UBERON:0002188 ! respiratory bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0004518 @@ -213423,8 +213644,8 @@ intersection_of: UBERON:0002049 ! vasculature intersection_of: has_part UBERON:0002391 ! lymph relationship: has_part UBERON:0002391 ! lymph relationship: part_of UBERON:0006558 ! lymphatic part of lymphoid system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI property_value: IAO:0000116 "consider merging with parent" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -213446,8 +213667,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -213466,9 +213687,9 @@ is_a: UBERON:0002113 ! kidney intersection_of: UBERON:0002113 ! kidney intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Left.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Left.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI [Term] id: UBERON:0004539 @@ -213486,9 +213707,9 @@ is_a: UBERON:0002113 ! kidney intersection_of: UBERON:0002113 ! kidney intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Right.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Right.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI [Term] id: UBERON:0004544 @@ -213531,8 +213752,8 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000970 ! eye intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI [Term] id: UBERON:0004549 @@ -213553,8 +213774,8 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000970 ! eye intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0004550 @@ -213808,7 +214029,7 @@ relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002178 UBERON:0001285 ! supplies nephron relationship: RO:0002252 UBERON:0004723 ! connecting branch of interlobular artery relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -213839,7 +214060,7 @@ relationship: capable_of GO:0003093 {source="Wikipedia"} ! regulation of glomeru relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002170 UBERON:0004212 ! connected to glomerular capillary relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -214160,7 +214381,7 @@ relationship: part_of UBERON:0005358 ! ventricle of nervous system relationship: RO:0002202 UBERON:0004060 ! develops from neural tube ventricular layer relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system relationship: RO:0002473 CL:0000065 ! composed primarily of ependymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray667.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray667.png" xsd:anyURI [Term] id: UBERON:0004673 @@ -214177,6 +214398,7 @@ xref: BIRNLEX:1346 xref: DHBA:12865 xref: DMBA:17739 xref: FMA:52610 +xref: HBA:9322 xref: SCTID:280185007 xref: TAO:0000192 xref: ZFA:0000192 @@ -214238,6 +214460,7 @@ xref: BIRNLEX:1588 xref: DHBA:12886 xref: DMBA:17750 xref: FMA:72632 +xref: HBA:9343 xref: neuronames:798 xref: UMLS:C0175555 is_a: UBERON:0006843 {source="FMA"} ! root of cranial nerve @@ -214324,7 +214547,7 @@ xref: ZFA:0001429 is_a: UBERON:0002616 ! regional part of brain relationship: capable_of GO:0001820 {source="Wikipedia"} ! serotonin secretion relationship: part_of UBERON:0002275 {source="GO", source="Wikipedia"} ! reticular formation -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI [Term] id: UBERON:0004688 @@ -214342,7 +214565,7 @@ xref: SCTID:244225009 xref: Wikipedia:Costocervical_trunk is_a: UBERON:0001637 ! artery relationship: RO:0002170 UBERON:0001533 ! connected to subclavian artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -214559,7 +214782,7 @@ xref: UMLS:C1284055 {source="ncithesaurus:Bulbus_Cordis"} xref: Wikipedia:Bulbus_cordis is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000948 ! heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship to bulbus arteriosus" xsd:string [Term] @@ -214676,7 +214899,7 @@ xref: Wikipedia:Jugular_vein is_a: UBERON:0001638 ! vein relationship: part_of UBERON:0000974 {gci_filler="NCBITaxon:8287", gci_relation="RO:0002162"} ! neck relationship: RO:0002179 UBERON:0000033 ! drains head -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png" xsd:anyURI [Term] id: UBERON:0004715 @@ -214698,7 +214921,7 @@ intersection_of: UBERON:0006444 ! annulus fibrosus intersection_of: part_of UBERON:0001066 ! intervertebral disk disjoint_from: UBERON:0006008 ! fibrous ring of heart relationship: part_of UBERON:0001066 ! intervertebral disk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI [Term] id: UBERON:0004716 @@ -214744,7 +214967,7 @@ xref: Wikipedia:Arcuate_vein is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel relationship: RO:0002170 UBERON:0009887 ! connected to interlobar vein -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -214768,7 +214991,7 @@ is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0004043 {source="MA"} ! semicircular canal ampulla relationship: RO:0002433 UBERON:0004043 ! contributes to morphology of semicircular canal ampulla -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png" xsd:anyURI [Term] id: UBERON:0004723 @@ -214794,7 +215017,7 @@ xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel disjoint_from: UBERON:0009885 {source="Wikipedia:Renal_circulation"} ! interlobar artery relationship: RO:0002170 UBERON:0001552 ! connected to kidney arcuate artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -214835,9 +215058,9 @@ is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002894 ! olfactory cortex relationship: RO:0002160 NCBITaxon:32523 {source="Wikipedia"} ! only in taxon Tetrapoda relationship: RO:0002433 UBERON:0002894 ! contributes to morphology of olfactory cortex -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Human_brainstem_anterior_view_2_description.JPG" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Human_brainstem_anterior_view_2_description.JPG" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -214866,7 +215089,7 @@ xref: MA:0002595 xref: Wikipedia:Vasa_recta is_a: UBERON:0001140 ! renal vein relationship: RO:0002170 UBERON:0004640 ! connected to renal efferent arteriole -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI property_value: IAO:0000116 "TODO - is this a vein or set of veins? in MA it is a venous blood vessel" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -214931,8 +215154,8 @@ is_a: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: part_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000116 "We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -214981,7 +215204,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -215295,7 +215518,7 @@ xref: MESH:D018483 xref: SCTID:361729006 xref: Wikipedia:Diaphysis is_a: UBERON:0005055 ! zone of long bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI [Term] id: UBERON:0004770 @@ -215350,7 +215573,7 @@ intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity intersection_of: RO:0002176 UBERON:0001728 ! connects nasopharynx relationship: part_of UBERON:0003128 ! cranium relationship: RO:0002176 UBERON:0001728 ! connects nasopharynx -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png" xsd:anyURI [Term] id: UBERON:0004775 @@ -215837,7 +216060,7 @@ is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0035965 ! wall of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg" xsd:anyURI [Term] id: UBERON:0004801 @@ -216291,7 +216514,7 @@ is_a: UBERON:0000115 ! lung epithelium is_a: UBERON:0000487 {source="FMA"} ! simple squamous epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: has_part CL:0002062 {source="FMA"} ! type I pneumocyte +relationship: has_part CL:0002062 {source="FMA"} ! pulmonary alveolar type 1 cell relationship: part_of UBERON:0004894 {source="FMA"} ! alveolar wall relationship: RO:0002433 UBERON:0000115 ! contributes to morphology of lung epithelium relationship: RO:0002433 UBERON:0002299 ! contributes to morphology of alveolus of lung @@ -216810,7 +217033,7 @@ xref: Wikipedia:Splanchnopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000925 ! endoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship to LPM" xsd:string [Term] @@ -216829,7 +217052,7 @@ xref: Wikipedia:Somatopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000924 ! ectoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI [Term] id: UBERON:0004875 @@ -216929,8 +217152,8 @@ intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002183 ! lobar bronchus relationship: has_part CL:0019019 ! tracheobronchial smooth muscle cell relationship: part_of UBERON:0002183 ! lobar bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0004889 @@ -217029,6 +217252,18 @@ intersection_of: part_of UBERON:0000164 ! primitive urogenital sinus relationship: part_of UBERON:0000164 ! primitive urogenital sinus relationship: RO:0002202 UBERON:0009846 {source="EHDAA2"} ! develops from embryonic cloacal epithelium +[Term] +id: UBERON:0004903 +name: bronchoalveolar duct junction +namespace: uberon +def: "A branch point connecting the respiratory bronchioles to the alveolar ducts[MP]." [MP:0004390] +subset: pheno_slim +xref: EMAPA:37448 {source="MA:th"} +is_a: UBERON:0007651 ! anatomical junction +relationship: part_of UBERON:0001004 ! respiratory system +relationship: RO:0002176 UBERON:0002173 ! connects pulmonary alveolar duct +relationship: RO:0002176 UBERON:0002188 ! connects respiratory bronchiole + [Term] id: UBERON:0004904 name: neuron projection bundle connecting eye with brain @@ -217042,7 +217277,7 @@ synonym: "optic nerve" BROAD [BTO:0000966] synonym: "optic nerve (generic)" EXACT [] xref: BTO:0000966 xref: EV:0100351 -xref: FBbt:00001956 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001956 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: TADS:0000232 is_a: UBERON:0000122 ! neuron projection bundle intersection_of: UBERON:0000122 ! neuron projection bundle @@ -217060,7 +217295,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -217178,7 +217413,7 @@ is_a: UBERON:0009497 ! epithelium of foregut-midgut junction is_a: UBERON:0009854 ! digestive tract diverticulum relationship: part_of UBERON:0002423 {source="EHDAA2"} ! hepatobiliary system relationship: RO:0002202 UBERON:0004161 {source="EHDAA2-modified"} ! develops from septum transversum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI [Term] id: UBERON:0004913 @@ -217213,7 +217448,7 @@ intersection_of: part_of UBERON:0001174 ! common bile duct intersection_of: part_of UBERON:0004914 ! duodenal papilla relationship: part_of UBERON:0001174 ! common bile duct relationship: part_of UBERON:0004914 ! duodenal papilla -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -217231,8 +217466,8 @@ xref: NCIT:C119578 xref: SCTID:245389007 is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0000320 ! duodenal mucosa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI [Term] id: UBERON:0004915 @@ -217259,7 +217494,7 @@ is_a: UBERON:0011185 ! gastrointestinal sphincter intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0004913 ! hepatopancreatic ampulla relationship: part_of UBERON:0004913 ! hepatopancreatic ampulla -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -217307,7 +217542,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -219092,7 +219327,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0002384 ! connective tissue relationship: overlaps UBERON:0003728 ! mediastinum relationship: part_of UBERON:0000473 ! testis -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI [Term] id: UBERON:0005055 @@ -219129,6 +219364,8 @@ is_a: UBERON:0004176 ! external genitalia intersection_of: UBERON:0004176 ! external genitalia intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009196 ! indifferent external genitalia +property_value: RO:0002175 NCBITaxon:50557 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005057 @@ -219446,7 +219683,7 @@ xref: Wikipedia:Descending_limb_of_loop_of_Henle is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2276" xsd:string @@ -219468,7 +219705,7 @@ xref: Wikipedia:Connecting_tubule is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0012275 ! meso-epithelium relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -219476,9 +219713,11 @@ id: UBERON:0005099 name: short descending thin limb namespace: uberon def: "The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology[GO]." [GO:0072063] +subset: human_reference_atlas is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0006914 ! squamous epithelium property_value: IAO:0000116 "TODO - epithelium types" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005100 @@ -219700,6 +219939,16 @@ intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0005151 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! metanephric proximal tubule property_value: IAO:0000116 "TODO - place mammalian xrefs here rather than at parent" xsd:string +[Term] +id: UBERON:0005126 +name: metanephric S1 +namespace: uberon +def: "The S1 portion is the initial portion of the metanephric proximal convoluted tubule and is responsible for avid reabsorption of water and solutes[GO]." [GO:0072231] +is_a: UBERON:0004196 ! proximal convoluted tubule segment 1 +intersection_of: UBERON:0004196 ! proximal convoluted tubule segment 1 +intersection_of: part_of UBERON:0000081 ! metanephros +relationship: part_of UBERON:0005124 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! metanephric proximal convoluted tubule + [Term] id: UBERON:0005127 name: metanephric thick ascending limb @@ -219937,7 +220186,7 @@ synonym: "invertebrate tracheal system" EXACT [] synonym: "open tracheal system" EXACT [] synonym: "tracheal system" BROAD SENSU [FBbt:00005024] xref: BTO:0003870 -xref: FBbt:00005024 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: SPD:0000427 xref: TADS:0000043 is_a: UBERON:0001004 ! respiratory system @@ -220000,7 +220249,7 @@ synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 -xref: FBbt:00007060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83115 is_a: UBERON:0000061 ! anatomical structure relationship: RO:0002473 GO:0005575 ! composed primarily of cellular_component @@ -220067,7 +220316,7 @@ is_a: UBERON:0014401 ! renal venous blood vessel disjoint_from: UBERON:0009887 ! interlobar vein relationship: part_of UBERON:0001225 ! cortex of kidney relationship: RO:0002170 UBERON:0004719 ! connected to kidney arcuate vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -221193,7 +221442,7 @@ xref: ZFA:0001261 is_a: UBERON:0000467 {source="ZFA"} ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI property_value: IAO:0000116 "TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity'" xsd:string [Term] @@ -221299,7 +221548,7 @@ xref: VHOG:0000456 xref: Wikipedia:Myelencephalon is_a: UBERON:0004733 ! segmental subdivision of hindbrain relationship: RO:0002495 UBERON:0010096 ! immediate transformation of future myelencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0005291 @@ -221363,7 +221612,7 @@ is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0004122 ! genitourinary system relationship: RO:0002202 UBERON:0004876 ! develops from urogenital fold -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png" xsd:anyURI property_value: IAO:0000116 "TODO - check developmental relationships. merge with urogenital ridge?" xsd:string [Term] @@ -221469,7 +221718,7 @@ intersection_of: part_of UBERON:0002411 ! clitoris relationship: adjacent_to UBERON:0006653 ! glans clitoris relationship: part_of UBERON:0002411 ! clitoris relationship: RO:0002494 UBERON:0035006 ! transformation of preputial swelling of female -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif" xsd:anyURI [Term] id: UBERON:0005309 @@ -221821,7 +222070,7 @@ is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0001000 ! vas deferens relationship: part_of UBERON:0004054 ! internal male genitalia relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI [Term] id: UBERON:0005356 @@ -222274,7 +222523,7 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000970 ! eye @@ -222664,7 +222913,7 @@ xref: SCTID:246901006 xref: Wikipedia:Adipose_capsule_of_kidney is_a: UBERON:0001013 ! adipose tissue relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - split perinephric / perirenal" xsd:string [Term] @@ -222683,7 +222932,7 @@ xref: neuronames:1242 xref: NLXANAT:20090312 xref: Wikipedia:Circumventricular_organs is_a: UBERON:0002616 ! regional part of brain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI [Term] id: UBERON:0005409 @@ -222919,7 +223168,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: BFO:0000004 @@ -223089,9 +223338,9 @@ xref: SCTID:244263001 xref: Wikipedia:Common_hepatic_artery is_a: UBERON:0004573 ! systemic artery relationship: RO:0002252 UBERON:0001640 ! connecting branch of celiac artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -223136,7 +223385,7 @@ intersection_of: part_of UBERON:0001677 ! sphenoid bone intersection_of: RO:0002570 UBERON:0000377 ! conduit for maxillary nerve relationship: part_of UBERON:0001677 ! sphenoid bone relationship: RO:0002570 UBERON:0000377 ! conduit for maxillary nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI [Term] id: UBERON:0005451 @@ -223182,7 +223431,7 @@ relationship: part_of UBERON:0001678 ! temporal bone relationship: RO:0002570 UBERON:0001586 ! conduit for internal jugular vein relationship: RO:0002570 UBERON:0001759 ! conduit for vagus nerve relationship: RO:0002570 UBERON:0002019 ! conduit for accessory XI nerve -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG" xsd:anyURI [Term] id: UBERON:0005457 @@ -223198,8 +223447,8 @@ is_a: UBERON:0005483 ! thymus lobe intersection_of: UBERON:0005483 ! thymus lobe intersection_of: BSPO:0000120 UBERON:0002370 ! thymus relationship: BSPO:0000120 UBERON:0002370 ! thymus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI [Term] id: UBERON:0005458 @@ -223279,7 +223528,7 @@ relationship: RO:0002202 UBERON:0010983 {source="EHDAA2"} ! develops from levato relationship: RO:0002371 UBERON:0002413 ! attached to cervical vertebra relationship: RO:0002372 UBERON:0001077 ! has muscle origin transverse process of vertebra relationship: RO:0002373 UBERON:0007174 ! has muscle insertion medial border of scapula -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bc/Levator_scapulae.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/bc/Levator_scapulae.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -223310,7 +223559,7 @@ intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002006 ! cortex of lymph node relationship: adjacent_to UBERON:0002194 ! capsule of lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -223327,8 +223576,8 @@ is_a: UBERON:0005483 ! thymus lobe intersection_of: UBERON:0005483 ! thymus lobe intersection_of: BSPO:0000121 UBERON:0002370 ! thymus relationship: BSPO:0000121 UBERON:0002370 ! thymus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI [Term] id: UBERON:0005470 @@ -223380,6 +223629,7 @@ id: UBERON:0005476 name: spinal nerve trunk namespace: uberon def: "Trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami." [http://orcid.org/0000-0002-6601-2165] +subset: human_reference_atlas synonym: "spinal nerve (trunk)" EXACT [FMA:5929] synonym: "spinal neural trunk" EXACT [FMA:5929] synonym: "trunk of spinal nerve" EXACT [FMA:5929] @@ -223389,6 +223639,7 @@ is_a: UBERON:0002464 ! nerve trunk intersection_of: UBERON:0002464 ! nerve trunk intersection_of: part_of UBERON:0001780 ! spinal nerve relationship: part_of UBERON:0001780 ! spinal nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005477 @@ -223469,7 +223720,7 @@ intersection_of: RO:0001025 UBERON:0002363 ! located in dura mater relationship: part_of UBERON:0003711 {source="FMA"} ! brachiocephalic vein relationship: part_of UBERON:0010743 ! meningeal cluster relationship: RO:0001025 UBERON:0002363 ! located in dura mater -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif" xsd:anyURI property_value: IAO:0000116 "the MA placement should be checked" xsd:string [Term] @@ -223501,7 +223752,7 @@ is_a: UBERON:0013140 ! systemic vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0001040 ! drains yolk sac relationship: RO:0002179 UBERON:0001040 ! drains yolk sac -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png" xsd:anyURI [Term] id: UBERON:0005491 @@ -224004,7 +224255,7 @@ xref: VHOG:0000351 xref: ZFA:0005133 is_a: UBERON:0003281 ! mesentery of stomach relationship: part_of UBERON:0009668 {source="EHDAA2"} ! ventral mesentery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png" xsd:anyURI [Term] id: UBERON:0005629 @@ -224599,7 +224850,7 @@ is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer is_a: UBERON:0005742 ! adventitia relationship: RO:0000086 PATO:0002462 ! has quality collagenous relationship: RO:0002473 UBERON:0011824 ! composed primarily of fibrous connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings" xsd:string [Term] @@ -224635,7 +224886,7 @@ xref: SCTID:30180000 xref: Wikipedia:Adventitia is_a: UBERON:0004923 ! organ component layer relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -224653,7 +224904,7 @@ is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI [Term] id: UBERON:0005745 @@ -224690,7 +224941,7 @@ relationship: BSPO:0000126 UBERON:0001677 {source="FMA-abduced-lr"} ! sphenoid b relationship: part_of UBERON:0002478 ! orbitosphenoid relationship: RO:0002570 UBERON:0000941 ! conduit for cranial nerve II relationship: RO:0002570 UBERON:0001619 ! conduit for ophthalmic artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8e/Orbita_mensch.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8e/Orbita_mensch.jpg" xsd:anyURI [Term] id: UBERON:0005749 @@ -224818,7 +225069,7 @@ is_a: UBERON:0003037 ! septum relationship: part_of UBERON:0001008 {source="MA"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png" xsd:anyURI property_value: IAO:0000116 "todo - use to define cloacal septation in GO" xsd:string [Term] @@ -224885,7 +225136,7 @@ intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: capable_of GO:0003094 ! glomerular filtration relationship: part_of UBERON:0004188 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! glomerular epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI [Term] id: UBERON:0005787 @@ -225024,7 +225275,7 @@ is_a: UBERON:0003513 ! trunk blood vessel relationship: part_of UBERON:0002201 ! vasculature of trunk relationship: RO:0002202 UBERON:0001917 ! develops from endothelium of artery relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png" xsd:anyURI [Term] id: UBERON:0005806 @@ -225260,7 +225511,7 @@ xref: Wikipedia:Maxillary_prominence is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: RO:0002202 UBERON:0007238 ! develops from 1st arch maxillary component -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI [Term] id: UBERON:0005870 @@ -225413,7 +225664,7 @@ relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external ge relationship: RO:0002160 NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! only in taxon Amniota relationship: RO:0002202 UBERON:0004874 ! develops from somatopleure relationship: RO:0002387 UBERON:0011757 ! has potential to develop into differentiated genital tubercle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png" xsd:anyURI [Term] id: UBERON:0005879 @@ -225441,7 +225692,7 @@ is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: adjacent_to UBERON:0004117 ! pharyngeal pouch relationship: overlaps UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0016545 ! pharyngeal ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg" xsd:anyURI property_value: IAO:0000116 "Note we use overlaps as the relationship to the arches" xsd:string [Term] @@ -225473,7 +225724,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: BSPO:0000098 UBERON:0005478 ! sulcus limitans of neural tube relationship: has_part CL:0000101 ! sensory neuron relationship: part_of UBERON:0004061 ! neural tube mantle layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray646.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray646.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/336" xsd:anyURI [Term] @@ -225620,7 +225871,7 @@ intersection_of: part_of UBERON:0000998 ! seminal vesicle relationship: channel_for UBERON:0010143 ! seminal vesicle fluid relationship: channels_into UBERON:0000999 ! ejaculatory duct relationship: part_of UBERON:0000998 ! seminal vesicle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png" xsd:anyURI [Term] id: UBERON:0005904 @@ -225823,7 +226074,7 @@ relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002170 UBERON:0002091 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! connected to appendicular skeleton relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -225978,11 +226229,11 @@ relationship: has_part CL:0002367 ! trabecular meshwork cell relationship: overlaps UBERON:0006206 ! iridocorneal angle relationship: part_of UBERON:0003956 ! aqueous drainage system relationship: RO:0002221 UBERON:0001766 ! surrounds anterior chamber of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI property_value: IAO:0000116 "TODO check syns - ligaments" xsd:string [Term] @@ -226154,7 +226405,7 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001040 ! supplies yolk sac relationship: RO:0002178 UBERON:0001040 ! supplies yolk sac relationship: RO:0002252 UBERON:0005805 ! connecting branch of dorsal aorta -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png" xsd:anyURI [Term] id: UBERON:0006003 @@ -226437,8 +226688,8 @@ relationship: part_of UBERON:0001255 ! urinary bladder relationship: RO:0002202 UBERON:0005760 {source="EHDAA2-modified"} ! develops from urorectal septum relationship: RO:0002202 UBERON:0009845 {source="EHDAA2"} ! develops from urogenital sinus mesenchyme relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -226692,7 +226943,7 @@ intersection_of: adjacent_to UBERON:0005805 ! dorsal aorta relationship: adjacent_to UBERON:0002333 ! pulmonary trunk relationship: adjacent_to UBERON:0005805 ! dorsal aorta relationship: RO:0002202 UBERON:0000095 {source="PMID:6844926", source="Wikipedia"} ! develops from cardiac neural crest -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png" xsd:anyURI [Term] id: UBERON:0006208 @@ -226751,7 +227002,7 @@ relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0006264 {source="EHDAA2"} ! mouth-foregut junction relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI [Term] id: UBERON:0006213 @@ -226849,7 +227100,7 @@ relationship: RO:0002202 UBERON:0004341 {source="Wikipedia"} ! develops from pri relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI [Term] id: UBERON:0006218 @@ -227308,7 +227559,7 @@ relationship: adjacent_to UBERON:0004067 ! lateral nasal prominence relationship: adjacent_to UBERON:0005868 ! maxillary prominence relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: RO:0002202 UBERON:0012313 {source="EHDAA2"} ! develops from 1st arch maxillary ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png" xsd:anyURI [Term] id: UBERON:0006267 @@ -228246,7 +228497,7 @@ intersection_of: RO:0002176 UBERON:0001046 ! connects hindgut relationship: part_of UBERON:0000159 ! anal canal relationship: RO:0002176 UBERON:0000931 ! connects proctodeum relationship: RO:0002176 UBERON:0001046 ! connects hindgut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png" xsd:anyURI [Term] id: UBERON:0006585 @@ -228408,7 +228659,7 @@ intersection_of: UBERON:0002213 ! cartilaginous joint intersection_of: RO:0002176 UBERON:0004742 {cardinality="2"} ! connects dentary relationship: part_of UBERON:0001710 ! lower jaw region relationship: RO:0002176 UBERON:0004742 ! connects dentary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI property_value: IAO:0000116 "this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints" xsd:string [Term] @@ -228430,7 +228681,7 @@ is_a: BFO:0000002 is_a: UBERON:0000158 {source="FMA"} ! membranous layer relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: part_of UBERON:0001630 {source="FMA"} ! muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Aponeurosis.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Aponeurosis.png" xsd:anyURI [Term] id: UBERON:0006615 @@ -228626,7 +228877,7 @@ intersection_of: UBERON:0035651 ! glans intersection_of: part_of UBERON:0002411 ! clitoris relationship: part_of UBERON:0002411 ! clitoris relationship: RO:0002202 UBERON:0013240 {source="cjm"} ! develops from future glans clitoris -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif" xsd:anyURI [Term] id: UBERON:0006657 @@ -228651,7 +228902,7 @@ xref: Wikipedia:Glenoid_cavity is_a: UBERON:0004704 ! bone fossa relationship: adjacent_to UBERON:0006849 ! scapula relationship: part_of UBERON:0004753 ! scapulocoracoid -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png" xsd:anyURI [Term] id: UBERON:0006658 @@ -228717,7 +228968,7 @@ xref: SCTID:368677009 xref: Wikipedia:Galea_aponeurotica is_a: UBERON:0006614 ! aponeurosis relationship: part_of UBERON:0000403 {source="FMA"} ! scalp -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI [Term] id: UBERON:0006668 @@ -228733,7 +228984,7 @@ intersection_of: UBERON:0013685 ! foramen of skull intersection_of: RO:0002570 UBERON:0001532 ! conduit for internal carotid artery relationship: part_of UBERON:0001678 ! temporal bone relationship: RO:0002570 UBERON:0001532 ! conduit for internal carotid artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png" xsd:anyURI [Term] id: UBERON:0006670 @@ -228848,7 +229099,7 @@ relationship: part_of UBERON:0001130 ! vertebral column relationship: RO:0002221 UBERON:0002240 ! surrounds spinal cord relationship: RO:0002570 UBERON:0002240 ! conduit for spinal cord relationship: RO:0002571 UBERON:0001130 ! lumen of vertebral column -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI property_value: IAO:0000116 "TODO - check neural vs vertebral canal; embryonic vs adult?" xsd:string [Term] @@ -228926,7 +229177,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0007223 {source="MA"} ! osseus cochlea relationship: RO:0002433 UBERON:0001844 ! contributes to morphology of cochlea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Gray921.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Gray921.png" xsd:anyURI [Term] id: UBERON:0006725 @@ -228973,7 +229224,7 @@ is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0006260 {source="EHDAA2"} ! lingual swellings relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI [Term] id: UBERON:0006757 @@ -228993,7 +229244,7 @@ is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0006260 ! lingual swellings relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI [Term] id: UBERON:0006761 @@ -229029,7 +229280,7 @@ intersection_of: RO:0002176 UBERON:0001773 ! connects sclera relationship: part_of UBERON:0000019 ! camera-type eye relationship: RO:0002176 UBERON:0000964 ! connects cornea relationship: RO:0002176 UBERON:0001773 ! connects sclera -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -229121,7 +229372,7 @@ name: lumen of open tracheal system trachea namespace: uberon def: "An anatomical space that surrounded_by a open tracheal system trachea." [OBOL:automatic] synonym: "tracheal lumen" BROAD SENSU [FBbt:00007410] -xref: FBbt:00007410 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007410 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space intersection_of: RO:0002572 UBERON:0003127 ! luminal space of open tracheal system trachea @@ -229150,7 +229401,7 @@ namespace: uberon def: "A subdivision of a the reproductive tract in a female organism that is the site of embryo development." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "uterus" BROAD SENSU [FBbt:00004924] -xref: FBbt:00004924 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004924 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: TADS:0000421 xref: WBbt:0006760 is_a: UBERON:0005156 ! reproductive structure @@ -229192,6 +229443,7 @@ subset: vertebrate_core synonym: "cranial nerve root" EXACT [FMA:52609] synonym: "cranial neural root" EXACT [FMA:52609] xref: FMA:52609 +xref: HBA:9299 xref: SCTID:280161004 xref: TAO:0002190 xref: ZFA:0001663 @@ -229262,7 +229514,7 @@ relationship: overlaps UBERON:0003692 {gci_relation="part_of", gci_filler="NCBIT relationship: part_of UBERON:0001467 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="FMA"} ! shoulder relationship: RO:0002202 UBERON:0004753 {source="ZFA"} ! develops from scapulocoracoid relationship: RO:0002202 UBERON:0006290 ! develops from scapula cartilage element -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -229384,7 +229636,7 @@ is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0000981 ! femur -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png" xsd:anyURI [Term] id: UBERON:0006863 @@ -229422,7 +229674,7 @@ def: "The distalmost portion of the digestive tract, derived from the hindgut, a synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" NARROW [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] -xref: FBbt:00005756 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005756 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0005773 is_a: BFO:0000002 is_a: UBERON:0004921 ! subdivision of digestive tract @@ -229436,7 +229688,7 @@ namespace: uberon def: "A gland that secretes a seminal fluid." [OBOL:automatic] subset: grouping_class subset: organ_slim -xref: FBbt:00004958 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004958 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006870 is_a: UBERON:0005399 ! male reproductive gland intersection_of: UBERON:0002530 ! gland @@ -229963,7 +230215,7 @@ relationship: channels_from UBERON:0003959 ! rete testis relationship: channels_into UBERON:0001301 ! epididymis relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI [Term] id: UBERON:0006947 @@ -229984,7 +230236,7 @@ relationship: BSPO:0000126 UBERON:0004054 {source="FMA-abduced-lr"} ! internal m relationship: channel_for UBERON:0001968 ! semen relationship: channels_from UBERON:0000473 ! testis relationship: part_of UBERON:0004054 ! internal male genitalia -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI [Term] id: UBERON:0006948 @@ -230227,7 +230479,7 @@ def: "A multicellular organism that existence_ends_with a post-juvenile adult st synonym: "adult" BROAD [] synonym: "adults" EXACT OMO:0003004 [TAO:0002046] xref: BILA:0000078 -xref: FBbt:00003004 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003004 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: galen:Adult xref: HAO:0000087 xref: http://neurolex.org/wiki/Category\:Adult_organism @@ -230345,7 +230597,7 @@ is_a: UBERON:0000478 ! extraembryonic structure is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003124 {source="BTO"} ! chorion membrane relationship: RO:0002202 UBERON:0004027 {source="MP-def"} ! develops from chorionic plate -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png" xsd:anyURI [Term] id: UBERON:0007119 @@ -230372,7 +230624,7 @@ is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0006863 ! proximal metaphysis of femur -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -231670,7 +231922,7 @@ relationship: part_of UBERON:0000017 {source="MA"} ! exocrine pancreas relationship: RO:0002170 UBERON:0000160 ! connected to intestine relationship: RO:0002202 UBERON:0003922 ! develops from pancreatic epithelial bud relationship: RO:0002433 UBERON:0000017 ! contributes to morphology of exocrine pancreas -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -231743,7 +231995,7 @@ synonym: "outer epidermal layer" EXACT [] synonym: "outer epithelial layer" EXACT [] xref: BSA:0000073 xref: BTO:0000313 -xref: FBbt:00004993 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004993 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000298 xref: TADS:0000109 xref: WBbt:0005733 @@ -232283,7 +232535,7 @@ xref: Wikipedia:Trigeminal_nerve_nuclei is_a: UBERON:0007245 {source="FMA"} ! nuclear complex of neuraxis relationship: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: overlaps UBERON:0003023 {source="FMA"} ! pontine tegmentum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI [Term] id: UBERON:0007644 @@ -232428,7 +232680,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -232483,7 +232735,7 @@ intersection_of: UBERON:0000161 ! orifice intersection_of: part_of UBERON:0001727 ! taste bud relationship: part_of UBERON:0001727 {source="FMA"} ! taste bud relationship: RO:0002150 UBERON:0000167 ! continuous with oral cavity -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg" xsd:anyURI [Term] id: UBERON:0007692 @@ -232942,7 +233194,7 @@ intersection_of: RO:0002576 UBERON:0001421 ! skeleton of pectoral girdle region relationship: part_of UBERON:0001421 ! pectoral girdle region relationship: part_of UBERON:0012475 ! skeleton of pectoral complex relationship: RO:0002576 UBERON:0001421 ! skeleton of pectoral girdle region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg" xsd:anyURI [Term] id: UBERON:0007832 @@ -232982,7 +233234,7 @@ relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex relationship: RO:0002202 UBERON:0010377 {source="PMID:21455939"} ! develops from mesenchyme from somatopleure relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string [Term] @@ -233193,7 +233445,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: has_part CL:0000312 ! keratinocyte relationship: part_of UBERON:0001705 {source="MA"} ! nail -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9f/Fingernail_label.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9f/Fingernail_label.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -233229,7 +233481,7 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0002355 ! luminal space of pelvic region of trunk relationship: part_of UBERON:0035819 ! abdominopelvic cavity relationship: RO:0002572 UBERON:0002355 ! luminal space of pelvic region of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0008229 @@ -233342,7 +233594,7 @@ intersection_of: UBERON:0000211 ! ligament intersection_of: part_of UBERON:0001758 ! periodontium relationship: part_of UBERON:0001758 {source="BTO"} ! periodontium relationship: RO:0002202 UBERON:0008969 {source="PMID:19767574", source="Wikipedia:Dental_follicle"} ! develops from dental follicle -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI property_value: seeAlso FMA:76870 [Term] @@ -233463,7 +233715,7 @@ is_a: UBERON:0005445 {source="FMA"} ! segment of pes is_a: UBERON:0008837 ! palmar/plantar part of autopod intersection_of: UBERON:0008837 ! palmar/plantar part of autopod intersection_of: part_of UBERON:0002387 ! pes -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/41/Soles2.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/41/Soles2.jpg" xsd:anyURI [Term] id: UBERON:0008339 @@ -233705,7 +233957,7 @@ intersection_of: UBERON:0000982 ! skeletal joint intersection_of: RO:0002176 UBERON:0001447 {cardinality="2"} ! connects tarsal bone relationship: part_of UBERON:0004454 ! tarsal region relationship: RO:0002176 UBERON:0001447 ! connects tarsal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png" xsd:anyURI [Term] id: UBERON:0008522 @@ -233834,7 +234086,7 @@ is_a: UBERON:0001638 {source="MA"} ! vein relationship: RO:0002170 UBERON:0001545 ! connected to anterior tibial vein relationship: RO:0002170 UBERON:0001547 ! connected to small saphenous vein relationship: RO:0002170 UBERON:0001550 ! connected to medial marginal vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -233900,7 +234152,7 @@ relationship: adjacent_to UBERON:0001091 ! calcareous tooth relationship: adjacent_to UBERON:0001828 ! gingiva relationship: part_of UBERON:0000165 ! mouth relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG" xsd:anyURI [Term] id: UBERON:0008811 @@ -233913,7 +234165,7 @@ synonym: "aedeagus" NARROW SENSU [FBbt:00004850] synonym: "copulatory organ" RELATED [] synonym: "penis" NARROW [] xref: AAO:0010255 -xref: FBbt:00004850 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004850 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000091 xref: TAO:0002036 xref: TGMA:0000585 @@ -233951,7 +234203,7 @@ namespace: uberon def: "A head that is part of a embryo." [OBOL:automatic] subset: non_informative xref: CALOHA:TS-0246 -xref: FBbt:00000155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293011 is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head @@ -234022,9 +234274,9 @@ xref: UMLS:C0034085 {source="ncithesaurus:Lung_Surfactant"} xref: Wikipedia:Pulmonary_surfactant is_a: UBERON:0006538 ! respiratory system fluid/secretion intersection_of: UBERON:0006538 ! respiratory system fluid/secretion -intersection_of: produced_by CL:0002063 ! type II pneumocyte +intersection_of: produced_by CL:0002063 ! pulmonary alveolar type 2 cell relationship: has_part CHEBI:6495 -relationship: produced_by CL:0002063 ! type II pneumocyte +relationship: produced_by CL:0002063 ! pulmonary alveolar type 2 cell [Term] id: UBERON:0008835 @@ -234048,7 +234300,7 @@ is_a: UBERON:0009497 ! epithelium of foregut-midgut junction is_a: UBERON:0009854 ! digestive tract diverticulum relationship: part_of UBERON:0004161 ! septum transversum relationship: RO:0002202 UBERON:0003894 {source="EHDAA2"} ! develops from liver primordium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI [Term] id: UBERON:0008836 @@ -234111,7 +234363,7 @@ relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secretin relationship: part_of UBERON:0001434 ! skeletal system relationship: RO:0002176 UBERON:0004765 ! connects skeletal element relationship: RO:0002473 UBERON:0007846 {source="VSAO"} ! composed primarily of dense regular connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI property_value: IAO:0000116 "logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71" xsd:string [Term] @@ -234168,7 +234420,7 @@ relationship: part_of UBERON:0001166 {source="Wikipedia"} ! pylorus relationship: RO:0002150 UBERON:0001165 ! continuous with pyloric antrum relationship: RO:0002150 UBERON:0001202 ! continuous with pyloric sphincter relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI [Term] id: UBERON:0008859 @@ -234217,7 +234469,7 @@ intersection_of: part_of UBERON:0001166 ! pylorus relationship: part_of UBERON:0004998 ! mucosa of pylorus relationship: RO:0000086 PATO:0002299 {source="Wikipedia:Tubular_gland"} ! has quality tubular relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png" xsd:anyURI property_value: IAO:0000116 "check relationship to pylorus vs antrum" xsd:string [Term] @@ -234231,13 +234483,13 @@ xref: EMAPA:37942 {source="MA:th"} is_a: UBERON:0008946 ! lung parenchyma intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: has_part CL:0002062 ! type I pneumocyte -relationship: has_part CL:0002063 ! type II pneumocyte +relationship: has_part CL:0002062 ! pulmonary alveolar type 1 cell +relationship: has_part CL:0002063 ! pulmonary alveolar type 2 cell relationship: has_part CL:0009089 ! lung pericyte relationship: part_of UBERON:0002299 ! alveolus of lung relationship: RO:0002433 UBERON:0006524 ! contributes to morphology of alveolar system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0008874 @@ -234259,8 +234511,8 @@ is_a: BFO:0000004 is_a: UBERON:0001062 ! anatomical entity relationship: part_of UBERON:0010369 ! secondary pulmonary lobule relationship: RO:0002170 UBERON:0002187 ! connected to terminal bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0008876 @@ -234328,7 +234580,7 @@ xref: VSAO:0000046 xref: Wikipedia:Osteoid xref: XAO:0004035 is_a: UBERON:0002481 {source="VSAO"} ! bone tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Active_osteoblasts.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Active_osteoblasts.jpg" xsd:anyURI [Term] id: UBERON:0008884 @@ -234341,8 +234593,8 @@ is_a: UBERON:0001874 ! putamen intersection_of: UBERON:0001874 ! putamen intersection_of: part_of UBERON:0002812 ! left cerebral hemisphere relationship: part_of UBERON:0002812 ! left cerebral hemisphere -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0008885 @@ -234355,8 +234607,8 @@ is_a: UBERON:0001874 ! putamen intersection_of: UBERON:0001874 ! putamen intersection_of: part_of UBERON:0002813 ! right cerebral hemisphere relationship: part_of UBERON:0002813 ! right cerebral hemisphere -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0008886 @@ -234392,7 +234644,7 @@ is_a: UBERON:0001593 {source="FMA"} ! venous plexus intersection_of: UBERON:0001593 ! venous plexus intersection_of: RO:0002221 UBERON:0001052 ! surrounds rectum relationship: RO:0002221 UBERON:0001052 ! surrounds rectum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png" xsd:anyURI [Term] id: UBERON:0008895 @@ -234423,7 +234675,7 @@ disjoint_from: UBERON:0011156 ! facial skeleton relationship: overlaps UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! facial skeleton relationship: RO:0002202 UBERON:0002539 {source="https://github.com/obophenotype/uberon/issues/83"} ! develops from pharyngeal arch relationship: RO:0002254 UBERON:0003099 ! has developmental contribution from cranial neural crest -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -234801,7 +235053,7 @@ intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus relationship: RO:0001025 UBERON:0001972 ! located in submucosa of esophagus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI [Term] id: UBERON:0008998 @@ -234964,7 +235216,7 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0001593 ! venous plexus intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -235157,6 +235409,7 @@ name: epibranchial ganglion namespace: uberon def: "Cranial ganglion which develops from an epibranchial placode." [PMID:20133851, ZFIN:curator] comment: Epibranchial ganglia orchestrate the development of the cranial neurogenic crest +subset: human_reference_atlas synonym: "epibranchial ganglia" EXACT OMO:0003004 [ZFA:0001555] xref: TAO:0001555 xref: ZFA:0001555 @@ -235165,6 +235418,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: RO:0002202 UBERON:0003078 ! develops from epibranchial placode relationship: RO:0002202 UBERON:0003078 {source="NCBIBook:NBK53175"} ! develops from epibranchial placode +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009128 @@ -235526,7 +235780,7 @@ xref: UMLS:C0004454 {source="ncithesaurus:Axilla"} xref: Wikipedia:Axilla is_a: UBERON:0034929 ! external soft tissue zone relationship: part_of UBERON:0001421 {source="FMA"} ! pectoral girdle region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png" xsd:anyURI [Term] id: UBERON:0009477 @@ -236350,6 +236604,7 @@ id: UBERON:0009623 name: spinal nerve root namespace: uberon def: "The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule." [MESH:A08.800.800.720.725] +subset: human_reference_atlas synonym: "root of spinal nerve" EXACT [FMA:14060] synonym: "spinal neural root" EXACT [FMA:14060] synonym: "spinal root" EXACT [BTO:0000883] @@ -236369,6 +236624,7 @@ relationship: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0002240 ! spinal cord relationship: RO:0002433 UBERON:0001780 ! contributes to morphology of spinal nerve relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2644" xsd:string [Term] @@ -237154,7 +237410,7 @@ intersection_of: RO:0000086 PATO:0002422 ! has quality acinar relationship: has_part CL:0000151 ! secretory cell relationship: part_of UBERON:0002530 ! gland relationship: RO:0000086 PATO:0002422 ! has quality acinar -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI [Term] id: UBERON:0009843 @@ -237261,7 +237517,7 @@ namespace: uberon def: "Branch or outpocketing of the digestive tract." [https://orcid.org/0000-0002-6601-2165] synonym: "diverticulum of gut" RELATED [FBbt:00100316] synonym: "intestinal pouch" RELATED [] -xref: FBbt:00100316 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0009856 ! sac intersection_of: UBERON:0009856 ! sac @@ -237294,7 +237550,7 @@ is_a: UBERON:0000158 ! membranous layer relationship: adjacent_to UBERON:0002484 ! bone marrow cavity relationship: part_of UBERON:0002495 ! long bone relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI [Term] id: UBERON:0009870 @@ -237315,7 +237571,7 @@ is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg" xsd:anyURI property_value: IAO:0000116 "We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach" xsd:string [Term] @@ -237446,7 +237702,7 @@ relationship: part_of UBERON:0001442 ! skeleton of manus relationship: part_of UBERON:0004452 ! carpal region relationship: proximally_connected_to UBERON:0010703 ! forelimb zeugopod skeleton relationship: RO:0002576 UBERON:0004452 ! skeleton of carpal region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI [Term] id: UBERON:0009881 @@ -237477,7 +237733,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0000159 ! anal canal relationship: RO:0000086 PATO:0001910 ! has quality folded -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI [Term] id: UBERON:0009883 @@ -237521,7 +237777,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0009913 ! supplies renal lobe relationship: RO:0002178 UBERON:0009913 ! supplies renal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -237542,7 +237798,7 @@ intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0009913 ! drains renal lobe relationship: RO:0002170 UBERON:0001140 ! connected to renal vein relationship: RO:0002179 UBERON:0009913 ! drains renal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -237637,7 +237893,7 @@ intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: IAO:0000116 "todo - add has_part relationships." xsd:string [Term] @@ -237988,7 +238244,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -238006,7 +238262,7 @@ def: "A small cluster of cells of various types which form a discrete structure, comment: Examples include arthropod sensilla. subset: upper_level xref: CARO:0010001 -xref: FBbt:00007229 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007229 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000062 {source="CARO"} ! organ is_a: UBERON:0034922 {source="CARO"} ! cell cluster disjoint_from: UBERON:0011216 {source="FBbt"} ! organ system subdivision @@ -238199,7 +238455,7 @@ intersection_of: part_of UBERON:0001723 {source="ISBN:1607950324"} ! tongue intersection_of: RO:0002202 UBERON:0006260 {source="ISBN:1607950324"} ! develops from lingual swellings relationship: part_of UBERON:0001723 ! tongue relationship: RO:0002202 UBERON:0006260 ! develops from lingual swellings -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Illu04_tongue.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Illu04_tongue.jpg" xsd:anyURI [Term] id: UBERON:0010038 @@ -238225,7 +238481,7 @@ intersection_of: part_of UBERON:0001160 ! fundus of stomach relationship: has_part CL:0000155 {source="ISBN:0073040584"} ! peptic cell relationship: has_part CL:0000162 {source="ISBN:0073040584"} ! parietal cell relationship: part_of UBERON:0004994 ! mucosa of fundus of stomach -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Fundic_gland_polyp_%281%29.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Fundic_gland_polyp_%281%29.jpg" xsd:anyURI property_value: IAO:0000116 "Consider FMA:14923 ! Principal gland of fundus of stomach. Added part_of to mucosa to be consistent with FMA pattern (note that Kardong places this in the glandular epithelium)" xsd:string [Term] @@ -238750,7 +239006,7 @@ intersection_of: RO:0002176 UBERON:0000209 ! connects tetrapod frontal bone intersection_of: RO:0002176 UBERON:0001677 ! connects sphenoid bone relationship: RO:0002176 UBERON:0000209 ! connects tetrapod frontal bone relationship: RO:0002176 UBERON:0001677 ! connects sphenoid bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png" xsd:anyURI [Term] id: UBERON:0010160 @@ -239355,7 +239611,7 @@ xref: Wikipedia:Lacrimal_punctum is_a: UBERON:0000161 {source="FMA"} ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001850 ! lacrimal drainage system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png" xsd:anyURI [Term] id: UBERON:0010285 @@ -239445,7 +239701,7 @@ subset: efo_slim synonym: "amnion-serosa" RELATED [BTO:0004800] xref: BTO:0004800 xref: EFO:0000250 -xref: FBbt:00000095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0010303 {source="DOI:10.1073/pnas.0709145105"} ! extraembryonic epithelium relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda property_value: IAO:0000116 "May be obsoleted once added to insect ontology. Coordinate with cell type in CL" xsd:string @@ -239834,7 +240090,7 @@ synonym: "ossification centre" EXACT [FMA:75436] xref: FMA:75436 xref: Wikipedia:Ossification_center is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fd/Gray79.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fd/Gray79.png" xsd:anyURI property_value: IAO:0000116 "currently classified as a zone of a bone organ, but exists prior to bone ossifying" xsd:string [Term] @@ -240011,8 +240267,8 @@ synonym: "respiratory lobule" RELATED [PMID:18403324] xref: FMA:7414 is_a: UBERON:0010368 {source="FMA"} ! pulmonary lobule relationship: part_of UBERON:0008946 {source="FMA"} ! lung parenchyma -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 [Term] id: UBERON:0010370 @@ -240238,8 +240494,8 @@ synonym: "efferent lymphatic vessels" RELATED [Wikipedia:Efferent_lymph_vessel] xref: MA:0000749 xref: Wikipedia:Efferent_lymph_vessel is_a: UBERON:0001473 ! lymphatic vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -240367,8 +240623,8 @@ is_a: UBERON:0010393 ! T cell domain intersection_of: UBERON:0010393 ! T cell domain intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0002006 {source="MP"} ! cortex of lymph node -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI [Term] id: UBERON:0010418 @@ -240498,11 +240754,11 @@ xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010428 @@ -240810,7 +241066,7 @@ disjoint_from: UBERON:0010545 {source="lexical"} ! metatarsus skeleton relationship: proximally_connected_to UBERON:0009880 ! carpal skeleton relationship: RO:0002202 UBERON:0010699 ! develops from manual digit metacarpus cartilage element relationship: RO:0002576 UBERON:0004453 ! skeleton of metacarpus region -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI [Term] id: UBERON:0010545 @@ -240842,7 +241098,7 @@ intersection_of: RO:0002576 UBERON:0000983 ! skeleton of metatarsus region relationship: proximally_connected_to UBERON:0009879 ! tarsal skeleton relationship: RO:0002202 UBERON:0010697 ! develops from pedal digit metatarsal cartilage element relationship: RO:0002576 UBERON:0000983 ! skeleton of metatarsus region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI [Term] id: UBERON:0010546 @@ -241148,8 +241404,8 @@ is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002328 GO:0040011 ! functionally related to locomotion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-04-23T10:46:51Z [Term] @@ -241370,8 +241626,8 @@ is_a: UBERON:0000444 ! lymphoid follicle intersection_of: UBERON:0000444 ! lymphoid follicle intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0002006 ! cortex of lymph node -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI [Term] id: UBERON:0010753 @@ -241410,7 +241666,7 @@ xref: UMLS:C0282491 {source="ncithesaurus:Germinal_Center"} xref: Wikipedia:Germinal_center is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0001745 ! secondary nodular lymphoid tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/60/Germinal_center.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/60/Germinal_center.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -241442,7 +241698,7 @@ def: "A major subdivision of an organism that divides an organism along an axis subset: upper_level synonym: "appendage segment" EXACT [FBbt:00007018] synonym: "appendicular segment" EXACT [] -xref: FBbt:00007018 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007018 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000026 ! appendage @@ -242059,6 +242315,7 @@ id: UBERON:0011096 name: lacrimal nerve namespace: uberon def: "The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve." [Wikipedia:Lacrimal_nerve] +subset: human_reference_atlas synonym: "nervus lacrimalis" EXACT OMO:0003011 [Wikipedia:Lacrimal_nerve] xref: FMA:52628 xref: NCIT:C32908 @@ -242070,6 +242327,7 @@ intersection_of: UBERON:0001021 ! nerve intersection_of: RO:0002134 UBERON:0001817 ! innervates lacrimal gland relationship: RO:0002134 UBERON:0001817 ! innervates lacrimal gland relationship: RO:0002380 UBERON:0000348 {source="FMA"} ! branching part of ophthalmic nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011107 @@ -242147,8 +242405,8 @@ intersection_of: RO:0002176 UBERON:0001447 ! connects tarsal bone intersection_of: RO:0002176 UBERON:0001448 ! connects metatarsal bone relationship: RO:0002176 UBERON:0001447 ! connects tarsal bone relationship: RO:0002176 UBERON:0001448 ! connects metatarsal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI [Term] id: UBERON:0011119 @@ -242170,7 +242428,7 @@ intersection_of: RO:0002176 UBERON:0001435 ! connects carpal bone intersection_of: RO:0002176 UBERON:0002374 ! connects metacarpal bone relationship: RO:0002176 UBERON:0001435 ! connects carpal bone relationship: RO:0002176 UBERON:0002374 ! connects metacarpal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png" xsd:anyURI [Term] id: UBERON:0011120 @@ -242221,7 +242479,7 @@ intersection_of: UBERON:0000982 ! skeletal joint intersection_of: RO:0002176 UBERON:0001435 {cardinality="2"} ! connects carpal bone relationship: part_of UBERON:0004452 {source="FMA"} ! carpal region relationship: RO:0002176 UBERON:0001435 ! connects carpal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png" xsd:anyURI [Term] id: UBERON:0011133 @@ -242236,7 +242494,7 @@ intersection_of: UBERON:0000982 ! skeletal joint intersection_of: RO:0002176 UBERON:0001448 {cardinality="2"} ! connects metatarsal bone relationship: part_of UBERON:0000983 ! metatarsus region relationship: RO:0002176 UBERON:0001448 ! connects metatarsal bone -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI [Term] id: UBERON:0011134 @@ -242394,7 +242652,7 @@ xref: Wikipedia:Facial_skeleton is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull relationship: part_of UBERON:0001456 {source="FMA"} ! face -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI [Term] id: UBERON:0011158 @@ -242504,9 +242762,9 @@ xref: EMAPA:19313 xref: Wikipedia:Ophthalmic_veins xref: XAO:0004169 is_a: UBERON:0009141 {source="EHDAA2-modified"} ! craniocervical region vein -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0011192 @@ -242523,7 +242781,7 @@ xref: SCTID:149481004 xref: Wikipedia:Superior_ophthalmic_vein is_a: UBERON:0011191 ! ophthalmic vein relationship: RO:0002170 UBERON:0003712 ! connected to cavernous sinus -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -242595,6 +242853,7 @@ xref: BIRNLEX:1456 xref: DHBA:12888 xref: DMBA:17748 xref: FMA:6213 +xref: HBA:9337 xref: ZFA:0007011 is_a: UBERON:0002211 ! nerve root intersection_of: UBERON:0002211 ! nerve root @@ -242637,7 +242896,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -243367,7 +243626,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0003716 ! recurrent laryngeal nerve intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg" xsd:anyURI [Term] id: UBERON:0011767 @@ -243869,6 +244128,7 @@ id: UBERON:0011925 name: preganglionic autonomic fiber namespace: uberon def: "Nerve fibers which project from the central nervous system to autonomic ganglia. In the sympathetic division most preganglionic fibers originate with neurons in the intermediolateral column of the spinal cord, exit via ventral roots from upper thoracic through lower lumbar segments, and project to the paravertebral ganglia; there they either terminate in synapses or continue through the splanchnic nerves to the prevertebral ganglia. In the parasympathetic division the fibers originate in neurons of the brain stem and sacral spinal cord. In both divisions the principal transmitter is acetylcholine but peptide cotransmitters may also be released." [MESH:A08.663.542.122, Wikipedia:Preganglionic_nerve_fibers] +subset: human_reference_atlas synonym: "preganglionic autonomic fibre" RELATED [] synonym: "preganglionic nerve fiber" EXACT [FMA:5923] xref: FMA:5923 @@ -243882,6 +244142,7 @@ intersection_of: extends_fibers_into UBERON:0001805 ! autonomic ganglion relationship: extends_fibers_into UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001805 ! autonomic ganglion relationship: part_of UBERON:0034728 ! autonomic nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011927 @@ -246474,7 +246735,7 @@ intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: RO:0002572 UBERON:0003129 ! luminal space of skull relationship: part_of UBERON:0003129 {source="Wikipedia"} ! skull relationship: RO:0002572 UBERON:0003129 ! luminal space of skull -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0013478 @@ -247300,7 +247561,7 @@ relationship: part_of UBERON:0012249 ! ectocervix relationship: RO:0002150 UBERON:0000996 ! continuous with vagina relationship: RO:0002176 UBERON:0000002 ! connects uterine cervix relationship: RO:0002176 UBERON:0000996 ! connects vagina -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI [Term] id: UBERON:0013761 @@ -247383,7 +247644,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002030 ! nipple intersection_of: BSPO:0000120 UBERON:0013702 ! body proper relationship: BSPO:0000120 UBERON:0013702 ! body proper -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-l.glb" xsd:anyURI [Term] id: UBERON:0013773 @@ -247397,7 +247658,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002030 ! nipple intersection_of: BSPO:0000121 UBERON:0013702 ! body proper relationship: BSPO:0000121 UBERON:0013702 ! body proper -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-r.glb" xsd:anyURI [Term] id: UBERON:0013774 @@ -247456,7 +247717,7 @@ is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer relationship: has_part CL:0000598 ! pyramidal neuron relationship: part_of UBERON:0004725 {source="NIFSTD"} ! piriform cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8406-3871 +property_value: terms:contributor https://orcid.org/0000-0002-8406-3871 [Term] id: UBERON:0014371 @@ -248036,6 +248297,7 @@ xref: BAMS:c11n xref: BIRNLEX:1580 xref: DHBA:12883 xref: DMBA:17749 +xref: HBA:9340 xref: neuronames:703 {source="BIRNLEX:1580"} xref: SCTID:280187004 xref: Wikipedia:Cranial_root_of_accessory_nerves @@ -248659,7 +248921,7 @@ relationship: adjacent_to UBERON:0001981 ! blood vessel relationship: adjacent_to UBERON:0002361 ! pia mater relationship: part_of UBERON:0010743 ! meningeal cluster relationship: RO:0001015 UBERON:0001359 ! location of cerebrospinal fluid -property_value: http://xmlns.com/foaf/0.1/depiction "https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif" xsd:anyURI +property_value: foaf:depiction "https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif" xsd:anyURI [Term] id: UBERON:0014935 @@ -249352,7 +249614,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -250159,8 +250421,8 @@ intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0002107 ! liver relationship: bounding_layer_of UBERON:0002107 ! liver relationship: RO:0002473 UBERON:0018135 ! composed primarily of fibrocollagenous connective tissue -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0016481 @@ -251356,8 +251618,8 @@ xref: SCTID:14885008 xref: Wikipedia:Internal_pudendal_veins is_a: UBERON:0009029 ! pudendal vein relationship: RO:0002170 UBERON:0001317 ! connected to internal iliac vein -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -251627,6 +251889,7 @@ id: UBERON:0018679 name: thoracic splanchnic nerve namespace: uberon def: "Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers." [Wikipedia:Thoracic_splanchnic_nerves] +subset: human_reference_atlas xref: FMA:6280 xref: Wikipedia:Thoracic_splanchnic_nerves is_a: UBERON:0003715 ! splanchnic nerve @@ -251635,6 +251898,7 @@ intersection_of: UBERON:0003715 ! splanchnic nerve intersection_of: RO:0002176 UBERON:0004863 ! connects thoracic sympathetic nerve trunk relationship: RO:0002176 UBERON:0004863 ! connects thoracic sympathetic nerve trunk relationship: RO:0002380 UBERON:0004863 {source="FMA"} ! branching part of thoracic sympathetic nerve trunk +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018685 @@ -251949,6 +252213,7 @@ synonym: "glossopharyngeal nerve root" EXACT [BIRNLEX:1533] xref: BIRNLEX:1533 xref: DHBA:12887 xref: DMBA:17747 +xref: HBA:9334 is_a: UBERON:0006843 ! root of cranial nerve intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001649 ! glossopharyngeal nerve @@ -252660,6 +252925,7 @@ id: UBERON:0034728 name: autonomic nerve namespace: uberon def: "The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa." [Wikipedia:Autonomic_nerve] +subset: human_reference_atlas synonym: "nervus visceralis" EXACT [FMA:5866] synonym: "visceral nerve" EXACT [FMA:5866] xref: EMAPA:37957 {source="MA:th"} @@ -252671,6 +252937,7 @@ is_a: UBERON:0011779 ! nerve of head region relationship: extends_fibers_into UBERON:0001805 ! autonomic ganglion relationship: part_of UBERON:0002410 ! autonomic nervous system relationship: RO:0002380 UBERON:0036264 ! branching part of zygomaticotemporal nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034729 @@ -252890,7 +253157,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -252918,7 +253185,7 @@ name: anatomical row namespace: uberon def: "An anatomical collection that is arranged in a line." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy -xref: FBbt:00100152 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100152 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034925 ! anatomical collection property_value: IAO:0000116 "resolve if this should be a subclass of or merged with aligned anatomical group." xsd:string property_value: RO:0002175 NCBITaxon:33090 @@ -253689,7 +253956,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001146 ! suprarenal vein intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism -relationship: RO:0002170 UBERON:0001072 ! connected to posterior vena cava +relationship: RO:0002170 UBERON:0001072 ! connected to inferior vena cava property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -253836,7 +254103,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001155 ! supplies colon relationship: RO:0002178 UBERON:0001155 ! supplies colon -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0035549 @@ -255112,8 +255379,8 @@ intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0001152 ! supplies cystic duct relationship: part_of UBERON:0015482 {source="FMA", source="Wikipedia"} ! right hepatic artery relationship: RO:0002178 UBERON:0001152 ! supplies cystic duct -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0039228 @@ -255170,7 +255437,7 @@ is_a: UBERON:0001145 {source="FMA"} ! ovarian vein intersection_of: UBERON:0001145 ! ovarian vein intersection_of: RO:0002179 UBERON:0002118 ! drains right ovary relationship: RO:0002179 UBERON:0002118 ! drains right ovary -relationship: RO:0002376 UBERON:0001072 {source="FMA"} ! tributary of posterior vena cava +relationship: RO:0002376 UBERON:0001072 {source="FMA"} ! tributary of inferior vena cava [Term] id: UBERON:0039857 @@ -255214,7 +255481,7 @@ is_a: UBERON:0001084 ! skin of head intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001456 ! face -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9611-1279 +property_value: terms:contributor https://orcid.org/0000-0002-9611-1279 creation_date: 2012-02-05T05:23:01Z [Term] @@ -255259,7 +255526,7 @@ is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: RO:0002176 UBERON:0004921 ! connects subdivision of digestive tract relationship: RO:0002176 UBERON:0004921 ! connects subdivision of digestive tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-02-05T11:19:31Z [Term] @@ -255729,7 +255996,7 @@ is_a: UBERON:0010328 ! limb bud mesenchyme intersection_of: UBERON:0010328 ! limb bud mesenchyme intersection_of: part_of UBERON:0005417 ! forelimb bud relationship: part_of UBERON:0005417 ! forelimb bud -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 +property_value: terms:contributor https://orcid.org/0000-0003-3162-7490 [Term] id: UBERON:4300227 @@ -255741,7 +256008,7 @@ is_a: UBERON:0010328 ! limb bud mesenchyme intersection_of: UBERON:0010328 ! limb bud mesenchyme intersection_of: part_of UBERON:0005418 ! hindlimb bud relationship: part_of UBERON:0005418 ! hindlimb bud -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 +property_value: terms:contributor https://orcid.org/0000-0003-3162-7490 [Term] id: UBERON:5001466 @@ -255839,7 +256106,7 @@ name: arthropod tagma namespace: uberon def: "One of the main divisions of the whole organism of arthropods formed from groups of segments." [doi:10.1016/B978-0-12-385026-3.00024-3] comment: Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods. -xref: FBbt:00000002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda property_value: RO:0002161 NCBITaxon:7742 @@ -255848,7 +256115,7 @@ property_value: RO:0002161 NCBITaxon:7742 id: UBERON:6000004 name: panarthropod head namespace: uberon -xref: FBbt:00000004 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000004 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head intersection_of: part_of NCBITaxon:88770 ! Panarthropoda @@ -255859,7 +256126,7 @@ id: UBERON:6000137 name: embryonic tagma namespace: uberon def: "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052)." [FBC:auto_generated_definition] -xref: FBbt:00000137 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0000922 ! embryo @@ -255870,7 +256137,7 @@ id: UBERON:6001728 name: insect larval tagma namespace: uberon def: "Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] -xref: FBbt:00001728 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001728 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0002548 ! larva @@ -255881,7 +256148,7 @@ id: UBERON:6001730 name: insect larval head namespace: uberon def: "Any head that is part of some larva." [FBC:auto_generated_definition] -xref: FBbt:00001730 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001730 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head intersection_of: part_of UBERON:0002548 ! larva @@ -255895,7 +256162,7 @@ name: insect larval sense organ namespace: uberon def: "Any sense organ that is part of some larva." [FBC:auto_generated_definition] synonym: "larval sense organ" EXACT [] -xref: FBbt:00002639 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00002639 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000020 ! sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: part_of UBERON:0002548 ! larva @@ -255908,7 +256175,7 @@ id: UBERON:6003005 name: insect adult tagma namespace: uberon def: "Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004)." [FBC:auto_generated_definition] -xref: FBbt:00003005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0007023 ! adult organism @@ -255919,7 +256186,7 @@ id: UBERON:6003007 name: insect adult head namespace: uberon def: "Head of the adult organism." [FBC:SPR] -xref: FBbt:00003007 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003007 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000004 ! panarthropod head is_a: UBERON:6003005 ! insect adult tagma intersection_of: UBERON:0000033 ! head @@ -255933,7 +256200,7 @@ name: insect embryonic/larval sensillum namespace: uberon def: "Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] synonym: "larval sensillum" EXACT [] -xref: FBbt:00007240 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007240 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0002536 ! arthropod sensillum is_a: UBERON:6002639 ! insect larval sense organ intersection_of: UBERON:0002536 ! arthropod sensillum @@ -255945,7 +256212,7 @@ name: insect embryonic/larval head sensillum namespace: uberon def: "Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] synonym: "larval head sensillum" NARROW [] -xref: FBbt:00007242 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007242 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000963 ! head sensillum is_a: UBERON:6007240 ! insect embryonic/larval sensillum is_a: UBERON:6007280 ! insect embryonic/larval head sense organ @@ -255958,7 +256225,7 @@ name: insect embryonic/larval head sense organ namespace: uberon def: "Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] synonym: "larval head sense organ" EXACT [] -xref: FBbt:00007280 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007280 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6002639 ! insect larval sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: part_of UBERON:6001730 ! insect larval head @@ -255976,7 +256243,7 @@ is_a: UBERON:4100000 ! skeletal element projection intersection_of: UBERON:0005813 ! tubercle intersection_of: part_of UBERON:0008772 ! proximal epiphysis of tibia relationship: part_of UBERON:0008772 ! proximal epiphysis of tibia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +property_value: terms:contributor https://orcid.org/0000-0003-2699-3066 [Term] id: UBERON:7500107 @@ -255989,8 +256256,8 @@ intersection_of: RO:0002176 UBERON:0001677 ! connects sphenoid bone intersection_of: RO:0002176 UBERON:0002396 ! connects vomer relationship: RO:0002176 UBERON:0001677 ! connects sphenoid bone relationship: RO:0002176 UBERON:0002396 ! connects vomer -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8415-4848 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 +property_value: terms:contributor https://orcid.org/0000-0001-8415-4848 +property_value: terms:contributor https://orcid.org/0000-0003-2699-3066 [Term] id: UBERON:8000006 @@ -256002,7 +256269,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001137 ! dorsum intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8000007 @@ -256014,7 +256281,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001137 ! dorsum intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8000009 @@ -256026,7 +256293,7 @@ is_a: UBERON:0010131 {source="https://github.com/obophenotype/uberon/issues/1785 is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle relationship: has_part UBERON:0002354 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! cardiac Purkinje fiber relationship: part_of UBERON:0004146 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! His-Purkinje system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8300000 @@ -256043,7 +256310,7 @@ is_a: UBERON:0001084 ! skin of head intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000403 ! scalp relationship: part_of UBERON:0000403 ! scalp -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300001 @@ -256056,7 +256323,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002102 ! forelimb intersection_of: BSPO:0000121 UBERON:0010708 ! pectoral complex relationship: BSPO:0000121 UBERON:0010708 ! pectoral complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300002 @@ -256069,7 +256336,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002102 ! forelimb intersection_of: BSPO:0000120 UBERON:0010708 ! pectoral complex relationship: BSPO:0000120 UBERON:0010708 ! pectoral complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300003 @@ -256082,7 +256349,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002103 ! hindlimb intersection_of: BSPO:0000121 UBERON:0010709 ! pelvic complex relationship: BSPO:0000121 UBERON:0010709 ! pelvic complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300004 @@ -256095,7 +256362,7 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002103 ! hindlimb intersection_of: BSPO:0000120 UBERON:0010709 ! pelvic complex relationship: BSPO:0000120 UBERON:0010709 ! pelvic complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 +property_value: terms:contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8400001 @@ -256106,8 +256373,8 @@ synonym: "hepatic acinus periportal zone" EXACT [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver relationship: overlaps UBERON:8400006 {xref="PMID:28126520"} ! liver lobule periportal region relationship: part_of UBERON:0001172 ! hepatic acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-09-08T14:14:21Z [Term] @@ -256121,8 +256388,8 @@ synonym: "hepatic acinus perivenous zone" EXACT [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver relationship: overlaps UBERON:8400007 {xref="PMID:28126520"} ! liver lobule centrilobular region relationship: part_of UBERON:0001172 ! hepatic acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-09-08T15:05:03Z [Term] @@ -256136,8 +256403,8 @@ relationship: adjacent_to UBERON:8400001 ! hepatic acinus zone 1 relationship: adjacent_to UBERON:8400002 ! hepatic acinus zone 3 relationship: overlaps UBERON:8400008 {xref="PMID:28126520"} ! liver lobule midzonal region relationship: part_of UBERON:0001172 ! hepatic acinus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-09-08T15:15:57Z [Term] @@ -256149,8 +256416,8 @@ synonym: "hepatic acinus metabolic zone" EXACT [PMID:8839925] is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-09-29T15:45:36Z [Term] @@ -256163,8 +256430,8 @@ is_a: UBERON:8400005 ! metabolic zone of liver relationship: adjacent_to UBERON:0001279 ! portal triad relationship: overlaps UBERON:8400001 {xref="PMID:28126520"} ! hepatic acinus zone 1 relationship: part_of UBERON:0004647 ! liver lobule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-10-05T12:56:57Z [Term] @@ -256177,8 +256444,8 @@ is_a: UBERON:8400005 ! metabolic zone of liver relationship: adjacent_to UBERON:0006841 ! central vein of liver relationship: overlaps UBERON:8400002 {xref="PMID:28126520"} ! hepatic acinus zone 3 relationship: part_of UBERON:0004647 ! liver lobule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-10-05T15:43:18Z [Term] @@ -256192,8 +256459,8 @@ relationship: adjacent_to UBERON:0001279 ! portal triad relationship: adjacent_to UBERON:0006841 ! central vein of liver relationship: overlaps UBERON:8400003 {xref="PMID:28126520"} ! hepatic acinus zone 2 relationship: part_of UBERON:0004647 ! liver lobule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X creation_date: 2020-10-05T15:52:22Z [Term] @@ -256208,7 +256475,7 @@ is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X [Term] id: UBERON:8400023 @@ -256225,7 +256492,7 @@ is_a: UBERON:0012375 ! subserosa intersection_of: UBERON:0012375 ! subserosa intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X [Term] id: UBERON:8400024 @@ -256240,7 +256507,7 @@ intersection_of: UBERON:0000353 ! parenchyma intersection_of: adjacent_to UBERON:0016479 ! capsule of liver intersection_of: part_of UBERON:0002107 ! liver relationship: adjacent_to UBERON:0016479 ! capsule of liver -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: terms:contributor https://orcid.org/0000-0003-2034-601X [Term] id: UBERON:8410000 @@ -256276,7 +256543,7 @@ is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001213 ! intestinal villus relationship: part_of UBERON:0001213 ! intestinal villus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410002 @@ -256289,7 +256556,7 @@ is_a: UBERON:0001473 ! lymphatic vessel intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410003 @@ -256304,8 +256571,8 @@ relationship: part_of UBERON:0002394 ! bile duct relationship: RO:0002221 UBERON:0002017 ! surrounds portal vein relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage relationship: RO:0002492 UBERON:0007220 ! existence ends during late embryonic stage -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:40674 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410004 @@ -256320,7 +256587,7 @@ is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001213 ! intestinal villus relationship: part_of UBERON:0001213 ! intestinal villus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410008 @@ -256332,7 +256599,7 @@ is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410009 @@ -256344,7 +256611,7 @@ is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410015 @@ -256355,7 +256622,7 @@ is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410016 @@ -256372,7 +256639,7 @@ intersection_of: RO:0002176 UBERON:0001159 ! connects sigmoid colon relationship: part_of UBERON:0000168 ! proximal-distal subdivision of colon relationship: RO:0002176 UBERON:0001158 ! connects descending colon relationship: RO:0002176 UBERON:0001159 ! connects sigmoid colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410017 @@ -256387,8 +256654,8 @@ intersection_of: RO:0002179 UBERON:0001158 ! drains descending colon intersection_of: RO:0002376 UBERON:0001215 ! tributary of inferior mesenteric vein relationship: RO:0002179 UBERON:0001158 ! drains descending colon relationship: RO:0002376 UBERON:0001215 ! tributary of inferior mesenteric vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410018 @@ -256403,8 +256670,8 @@ intersection_of: RO:0002179 UBERON:0001156 ! drains ascending colon intersection_of: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein relationship: RO:0002179 UBERON:0001156 ! drains ascending colon relationship: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410019 @@ -256419,7 +256686,7 @@ intersection_of: RO:0002176 UBERON:0002116 ! connects ileum relationship: part_of UBERON:0002108 ! small intestine relationship: RO:0002176 UBERON:0002115 ! connects jejunum relationship: RO:0002176 UBERON:0002116 ! connects ileum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410020 @@ -256432,7 +256699,7 @@ is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410024 @@ -256445,7 +256712,7 @@ intersection_of: UBERON:0007651 ! anatomical junction intersection_of: part_of UBERON:0000160 ! intestine intersection_of: RO:0002176 UBERON:0004921 ! connects subdivision of digestive tract relationship: part_of UBERON:0000160 ! intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410028 @@ -256460,7 +256727,7 @@ is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410030 @@ -256473,7 +256740,7 @@ is_a: UBERON:0001473 ! lymphatic vessel intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410032 @@ -256488,8 +256755,8 @@ intersection_of: adjacent_to UBERON:0002195 ! trabecula of lymph node intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002195 ! trabecula of lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410033 @@ -256503,8 +256770,8 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0000029 ! drains lymph node relationship: RO:0002179 UBERON:0000029 ! drains lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410034 @@ -256532,8 +256799,8 @@ intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0002007 ! medulla of lymph node relationship: part_of UBERON:0002007 ! medulla of lymph node relationship: RO:0002252 UBERON:8410034 ! connecting branch of lymph node artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410036 @@ -256546,8 +256813,8 @@ is_a: UBERON:8410041 ! venule of lymph node intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0002007 ! medulla of lymph node relationship: part_of UBERON:0002007 ! medulla of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410037 @@ -256558,7 +256825,7 @@ synonym: "HEV" BROAD OMO:0003000 [] xref: BTO:0004528 xref: NCIT:C32739 is_a: UBERON:0035428 ! postcapillary venule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410038 @@ -256571,8 +256838,8 @@ is_a: UBERON:8410037 ! high endothelial venule is_a: UBERON:8410041 ! venule of lymph node intersection_of: UBERON:8410037 ! high endothelial venule intersection_of: part_of UBERON:0000029 ! lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410039 @@ -256586,7 +256853,7 @@ is_a: UBERON:8410020 ! venule of appendix is_a: UBERON:8410037 ! high endothelial venule intersection_of: UBERON:8410037 ! high endothelial venule intersection_of: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410040 @@ -256599,7 +256866,7 @@ is_a: UBERON:8410037 ! high endothelial venule intersection_of: UBERON:8410037 ! high endothelial venule intersection_of: part_of UBERON:0003454 ! small intestine Peyer's patch relationship: part_of UBERON:0003454 ! small intestine Peyer's patch -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410041 @@ -256612,8 +256879,8 @@ is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410042 @@ -256626,8 +256893,8 @@ is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0000029 ! lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410043 @@ -256643,8 +256910,8 @@ is_a: UBERON:8410077 ! airway submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410044 @@ -256657,7 +256924,7 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410045 @@ -256670,7 +256937,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410046 @@ -256684,7 +256951,7 @@ is_a: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410047 @@ -256698,7 +256965,7 @@ is_a: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410048 @@ -256709,7 +256976,7 @@ is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410049 @@ -256728,7 +256995,7 @@ is_a: UBERON:0006134 ! nerve fiber intersection_of: UBERON:0006134 ! nerve fiber intersection_of: part_of UBERON:0012498 ! serosa of appendix relationship: part_of UBERON:0012498 ! serosa of appendix -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410050 @@ -256746,9 +257013,9 @@ relationship: has_part UBERON:0000159 ! anal canal relationship: has_part UBERON:0001052 ! rectum relationship: has_part UBERON:0001245 ! anus relationship: part_of UBERON:0000059 ! large intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: IAO:0000116 "The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum." xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410051 @@ -256759,7 +257026,7 @@ is_a: UBERON:0001473 ! lymphatic vessel intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410052 @@ -256772,8 +257039,8 @@ synonym: "light zone of germinal center" BROAD [] synonym: "light zone of lymph node germinal center" EXACT [] is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0009039 ! lymph node germinal center -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410053 @@ -256786,8 +257053,8 @@ synonym: "dark zone of lymph node germinal center" EXACT [] synonym: "germinal center dark zone" BROAD [] is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0009039 ! lymph node germinal center -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410056 @@ -256799,7 +257066,7 @@ is_a: UBERON:0001982 ! capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:8410050 ! anorectum relationship: part_of UBERON:8410050 ! anorectum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410057 @@ -256811,7 +257078,7 @@ is_a: UBERON:0001982 ! capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410060 @@ -256824,7 +257091,7 @@ intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0001155 ! colon intersection_of: part_of UBERON:0004220 ! large intestine smooth muscle relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410061 @@ -256837,7 +257104,7 @@ intersection_of: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: part_of UBERON:0001155 ! colon intersection_of: part_of UBERON:0004220 ! large intestine smooth muscle relationship: part_of UBERON:0001155 ! colon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410065 @@ -256849,7 +257116,7 @@ synonym: "marginal zone of lymph node" BROAD [] synonym: "marginal zone of lymph node follicle" EXACT [] is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0000029 ! lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410066 @@ -256859,8 +257126,8 @@ def: "The lymph node paracortex is the middle layer of the lymph node and is mos subset: human_reference_atlas is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0010417 ! lymph node T cell domain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410068 @@ -256874,8 +257141,8 @@ is_a: UBERON:0001982 ! capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2021-12-21T15:14:31Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2021-12-21T15:14:31Z" xsd:dateTime [Term] id: UBERON:8410071 @@ -256889,9 +257156,9 @@ synonym: "subcapsular sinus of lymph node ceiling" EXACT [] is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node relationship: part_of UBERON:0002194 ! capsule of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-22T17:04:49Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-22T17:04:49Z" xsd:dateTime [Term] id: UBERON:8410072 @@ -256905,9 +257172,9 @@ synonym: "subcapsular sinus of lymph node floor" EXACT [] is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node relationship: part_of UBERON:0002006 ! cortex of lymph node -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-02-22T17:16:40Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-02-22T17:16:40Z" xsd:dateTime [Term] id: UBERON:8410077 @@ -256923,8 +257190,8 @@ is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000065 ! respiratory tract -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 -property_value: http://purl.org/dc/terms/date "2022-03-24T14:21:59Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:date "2022-03-24T14:21:59Z" xsd:dateTime [Term] id: UBERON:8410080 @@ -256960,7 +257227,7 @@ is_a: UBERON:0016446 ! hair of head intersection_of: UBERON:0001037 ! strand of hair intersection_of: part_of UBERON:0000403 ! scalp relationship: part_of UBERON:0000403 ! scalp -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 +property_value: terms:contributor https://orcid.org/0000-0001-8314-2140 [Term] id: UBERON:8440000 @@ -257033,7 +257300,7 @@ intersection_of: capable_of_part_of GO:0007601 ! visual perception intersection_of: part_of UBERON:0000956 ! cerebral cortex relationship: capable_of_part_of GO:0007601 ! visual perception relationship: part_of UBERON:0000956 ! cerebral cortex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8440015 @@ -257050,7 +257317,7 @@ namespace: uberon def: "A structure embedded in the superior olivary complex that is driven by input pathways from the octopus cells in the cochlear nucleus and the neurons of the medial nucleus of the trapezoid body." [DOI:10.1093/oxfordhb/9780190849061.013.11] synonym: "SPON" EXACT [DOI:10.1093/oxfordhb/9780190849061.013.11] is_a: UBERON:0007247 ! nucleus of superior olivary complex -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8450001 @@ -257060,9 +257327,9 @@ def: "An individual reproductive unit containing a single oocyte and one or seve is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000992 ! ovary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 -property_value: http://purl.org/dc/terms/date "2022-04-19T11:08:10Z" xsd:dateTime property_value: seeAlso "https://github.com/obophenotype/uberon/issues/476" xsd:anyURI +property_value: terms:contributor https://orcid.org/0000-0002-6095-8718 +property_value: terms:date "2022-04-19T11:08:10Z" xsd:dateTime [Term] id: UBERON:8450002 @@ -257087,7 +257354,7 @@ is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood intersection_of: RO:0001025 UBERON:0001987 ! located in placenta relationship: RO:0001025 UBERON:0001987 ! located in placenta -property_value: http://purl.org/dc/terms/date "2022-04-04T11:06:09Z" xsd:dateTime +property_value: terms:date "2022-04-04T11:06:09Z" xsd:dateTime [Term] id: UBERON:8480000 @@ -257098,8 +257365,8 @@ is_a: UBERON:0004696 ! venous system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0005610 ! iliac vein relationship: part_of UBERON:0005610 ! iliac vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-17T14:34:50Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-17T14:34:50Z" xsd:dateTime [Term] id: UBERON:8480001 @@ -257110,8 +257377,8 @@ is_a: UBERON:0001982 ! capillary is_a: UBERON:0003499 ! brain blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0000955 ! brain -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T09:28:31Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T09:28:31Z" xsd:dateTime [Term] id: UBERON:8480002 @@ -257122,8 +257389,8 @@ is_a: UBERON:0004178 ! aorta smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001515 ! thoracic aorta relationship: part_of UBERON:0001515 ! thoracic aorta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T09:30:54Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T09:30:54Z" xsd:dateTime [Term] id: UBERON:8480003 @@ -257134,8 +257401,8 @@ is_a: UBERON:0002111 ! artery smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0005609 ! iliac artery relationship: part_of UBERON:0005609 ! iliac artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T09:32:07Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T09:32:07Z" xsd:dateTime [Term] id: UBERON:8480004 @@ -257146,8 +257413,8 @@ is_a: UBERON:0001919 ! endothelium of vein intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0005610 ! iliac vein relationship: part_of UBERON:0005610 ! iliac vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T09:33:18Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T09:33:18Z" xsd:dateTime [Term] id: UBERON:8480005 @@ -257160,8 +257427,8 @@ is_a: UBERON:0005292 ! extraembryonic tissue intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:8480007 ! placental artery relationship: part_of UBERON:8480007 ! placental artery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T09:34:25Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T09:34:25Z" xsd:dateTime [Term] id: UBERON:8480006 @@ -257173,8 +257440,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0002095 ! mesentery relationship: part_of UBERON:0002095 ! mesentery -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T09:35:29Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T09:35:29Z" xsd:dateTime [Term] id: UBERON:8480007 @@ -257185,8 +257452,8 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0022358 ! placenta blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-24T11:25:24Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-24T11:25:24Z" xsd:dateTime [Term] id: UBERON:8480008 @@ -257197,8 +257464,8 @@ is_a: UBERON:0001638 ! vein is_a: UBERON:0022358 ! placenta blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-06-27T09:30:52Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-06-27T09:30:52Z" xsd:dateTime [Term] id: UBERON:8480025 @@ -257209,8 +257476,8 @@ is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001421 ! pectoral girdle region relationship: part_of UBERON:0001421 ! pectoral girdle region -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-08-29T14:17:12Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-08-29T14:17:12Z" xsd:dateTime [Term] id: UBERON:8480026 @@ -257223,8 +257490,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0007830 ! pelvic girdle bone/zone relationship: part_of UBERON:0007830 ! pelvic girdle bone/zone -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-08-29T14:19:16Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-08-29T14:19:16Z" xsd:dateTime [Term] id: UBERON:8480029 @@ -257236,8 +257503,8 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0004176 ! external genitalia relationship: part_of UBERON:0004176 ! external genitalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-08-30T06:55:06Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-08-30T06:55:06Z" xsd:dateTime [Term] id: UBERON:8480030 @@ -257248,8 +257515,8 @@ is_a: UBERON:0001868 ! skin of chest intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000310 ! breast relationship: part_of UBERON:0000310 ! breast -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-08-29T14:03:54Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-08-29T14:03:54Z" xsd:dateTime [Term] id: UBERON:8480037 @@ -257264,8 +257531,8 @@ is_a: UBERON:0012375 ! subserosa intersection_of: UBERON:0012375 ! subserosa intersection_of: part_of UBERON:0003889 ! fallopian tube relationship: part_of UBERON:0003889 ! fallopian tube -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2022-10-21T08:55:11Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2022-10-21T08:55:11Z" xsd:dateTime [Term] id: UBERON:8480068 @@ -257276,8 +257543,8 @@ is_a: UBERON:0004696 ! venous system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0007318 ! saphenous vein relationship: part_of UBERON:0007318 ! saphenous vein -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-08-31T11:41:09Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-08-31T11:41:09Z" xsd:dateTime [Term] id: UBERON:8480074 @@ -257289,8 +257556,8 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000991 ! gonad relationship: part_of UBERON:0000991 ! gonad -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 -property_value: http://purl.org/dc/terms/date "2023-08-29T10:24:24Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:date "2023-08-29T10:24:24Z" xsd:dateTime [Term] id: UBERON:8600000 @@ -257300,9 +257567,9 @@ def: "A conductive airway that branches into terminal bronchioles." [PMID:165435 subset: human_reference_atlas synonym: "preterminal bronchiole" EXACT [PMID:16543587] is_a: UBERON:0002186 ! bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-08T13:31:12Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-08T13:31:12Z" xsd:dateTime [Term] id: UBERON:8600001 @@ -257315,8 +257582,8 @@ is_a: UBERON:0002051 ! epithelium of bronchiole intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:8600000 ! lobular bronchiole relationship: part_of UBERON:8600000 ! lobular bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-10T14:26:09Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-10T14:26:09Z" xsd:dateTime [Term] id: UBERON:8600002 @@ -257327,8 +257594,8 @@ is_a: UBERON:0005039 ! mucosa of bronchiole intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:8600000 ! lobular bronchiole relationship: part_of UBERON:8600000 ! lobular bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-10T14:48:35Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-10T14:48:35Z" xsd:dateTime [Term] id: UBERON:8600003 @@ -257339,8 +257606,8 @@ is_a: UBERON:0004515 ! smooth muscle tissue of bronchiole intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:8600000 ! lobular bronchiole relationship: part_of UBERON:8600000 ! lobular bronchiole -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-10T14:54:06Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-10T14:54:06Z" xsd:dateTime [Term] id: UBERON:8600004 @@ -257351,8 +257618,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Term] id: UBERON:8600006 @@ -257362,8 +257629,8 @@ def: "A striated muscle tissue that is associated with soft internal organs (vis synonym: "striated visceral muscle tissue" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:8600004 ! visceral muscle tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:34:43Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:34:43Z" xsd:dateTime [Term] id: UBERON:8600010 @@ -257376,10 +257643,10 @@ is_a: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:8410043 ! bronchus submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-05-02T08:07:56Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-05-02T08:07:56Z" xsd:dateTime [Term] id: UBERON:8600011 @@ -257392,10 +257659,10 @@ is_a: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: part_of UBERON:0005203 ! trachea gland relationship: part_of UBERON:0005203 ! trachea gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-05-02T08:08:14Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-05-02T08:08:14Z" xsd:dateTime [Term] id: UBERON:8600012 @@ -257407,9 +257674,9 @@ is_a: UBERON:0014717 ! mucous acinus intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0011148 ! submucosal gland relationship: part_of UBERON:0011148 ! submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-05-02T08:57:27Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-05-02T08:57:27Z" xsd:dateTime [Term] id: UBERON:8600014 @@ -257419,8 +257686,8 @@ def: "A ciliated tubular structure in a submucosal gland connecting the submucos is_a: UBERON:0000058 ! duct relationship: has_part CL:0000067 ! ciliated epithelial cell relationship: part_of UBERON:0011148 ! submucosal gland -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-05-02T08:09:14Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-05-02T08:09:14Z" xsd:dateTime [Term] id: UBERON:8600017 @@ -257434,10 +257701,10 @@ is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000101 ! lobe of lung relationship: RO:0002433 UBERON:0000101 ! contributes to morphology of lobe of lung -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 -property_value: http://purl.org/dc/terms/date "2023-07-20T12:43:29Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0002-9185-3994 +property_value: terms:date "2023-07-20T12:43:29Z" xsd:dateTime [Term] id: UBERON:8600018 @@ -257449,8 +257716,8 @@ synonym: "NES" RELATED OMO:0003000 [PMID:15481802] is_a: UBERON:0000467 ! anatomical system relationship: overlaps UBERON:0000949 ! endocrine system relationship: overlaps UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-29T10:49:45Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-29T10:49:45Z" xsd:dateTime [Term] id: UBERON:8600021 @@ -257462,9 +257729,9 @@ is_a: UBERON:0022358 ! placenta blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004027 ! chorionic plate relationship: part_of UBERON:0004027 ! chorionic plate -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-09-14T09:09:36Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-09-14T09:09:36Z" xsd:dateTime [Term] id: UBERON:8600023 @@ -257478,9 +257745,9 @@ is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0007106 ! chorionic villus relationship: part_of UBERON:0007106 ! chorionic villus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 -property_value: http://purl.org/dc/terms/date "2023-07-04T10:46:17Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:date "2023-07-04T10:46:17Z" xsd:dateTime [Term] id: UBERON:8600024 @@ -257495,8 +257762,8 @@ intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0013127 ! pulmonary venous system relationship: RO:0002170 UBERON:0002016 ! connected to pulmonary vein relationship: RO:0002179 UBERON:0016405 ! drains pulmonary capillary -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-10-24T11:26:27Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-10-24T11:26:27Z" xsd:dateTime [Term] id: UBERON:8600034 @@ -257509,9 +257776,9 @@ is_a: UBERON:0001238 ! lamina propria of small intestine intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0008343 ! intestinal villus of jejunum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8134-3037 -property_value: http://purl.org/dc/terms/date "2024-01-09T16:36:35Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-8134-3037 +property_value: terms:date "2024-01-09T16:36:35Z" xsd:dateTime [Term] id: UBERON:8600035 @@ -257524,47 +257791,53 @@ is_a: UBERON:0001238 ! lamina propria of small intestine intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002116 ! ileum relationship: part_of UBERON:0008344 ! intestinal villus of ileum -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8134-3037 -property_value: http://purl.org/dc/terms/date "2024-01-09T16:48:17Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:contributor https://orcid.org/0000-0001-8134-3037 +property_value: terms:date "2024-01-09T16:48:17Z" xsd:dateTime [Term] id: UBERON:8600038 name: placental disc namespace: uberon def: "A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier." [PMID:35496035] +subset: human_reference_atlas synonym: "placental disk" EXACT [PMID:30133439] is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001987 ! placenta -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2024-01-16T17:50:20Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-01-16T17:50:20Z" xsd:dateTime [Term] id: UBERON:8600039 name: chorionic villous mesenchyme namespace: uberon def: "A mesenchyme that is part of a chorionic villus." [doi:10.1007/978-3-030-84725-8] +subset: human_reference_atlas is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003265 ! chorionic mesenchyme is_a: UBERON:0010377 ! mesenchyme from somatopleure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0007106 ! chorionic villus relationship: part_of UBERON:0007106 ! chorionic villus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2024-01-16T18:13:12Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-01-16T18:13:12Z" xsd:dateTime [Term] id: UBERON:8600042 name: endometrial lymphatic vessel namespace: uberon def: "A lymphatic vessel that is part of an endometrium." [PMID:23054374] +subset: human_reference_atlas is_a: UBERON:0001473 ! lymphatic vessel is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0001295 ! endometrium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2024-01-16T18:18:36Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-01-16T18:18:36Z" xsd:dateTime [Term] id: http://purl.obolibrary.org/obo/D96882F1-8709-49AB-BCA9-772A67EA6C33 @@ -258681,8 +258954,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -258690,8 +258963,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -258700,8 +258973,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -258859,16 +259132,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -258878,6 +259155,7 @@ def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. is_a: BSPO:0000100 is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -258895,6 +259173,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -259120,6 +259399,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -259598,18 +259878,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/patterns/definitions.owl b/patterns/definitions.owl index 046777e53..ccbcd836b 100644 --- a/patterns/definitions.owl +++ b/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-02-13") + +Annotation(owl:versionInfo "2024-07-09") diff --git a/src/ontology/reports/cl-base-diff.md b/src/ontology/reports/cl-base-diff.md new file mode 100644 index 000000000..266f7f180 --- /dev/null +++ b/src/ontology/reports/cl-base-diff.md @@ -0,0 +1,7183 @@ +# Ontology comparison + +## Left +- Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-05-15/cl-base.owl/cl/cl-base.owl` +- Loaded from: `file:/work/src/ontology/tmp/current-base-release.obo` + +## Right +- Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-07-10/cl-base.owl/cl/cl-base.owl` +- Loaded from: `file:/work/src/ontology/../../cl-base.obo` + +### Ontology imports + + + +### Ontology annotations +#### Removed +- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-05-15"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [comment](http://www.w3.org/2000/01/rdf-schema#comment) "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo."^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-07-10"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [comment](http://www.w3.org/2000/01/rdf-schema#comment) "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo."^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Ammon's horn basket cell `http://purl.obolibrary.org/obo/CL_2000088` +#### Removed +- [Ammon's horn basket cell](http://purl.obolibrary.org/obo/CL_2000088) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [Ammon's horn basket cell](http://purl.obolibrary.org/obo/CL_2000088) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### B cell `http://purl.obolibrary.org/obo/CL_0000236` +#### Removed +- [B cell](http://purl.obolibrary.org/obo/CL_0000236) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009142"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [B cell](http://purl.obolibrary.org/obo/CL_0000236) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009142"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### BDS_subset `http://purl.obolibrary.org/obo/cl/cl-base#BDS_subset` + +#### Added +- [BDS_subset](http://purl.obolibrary.org/obo/cl/cl-base#BDS_subset) [comment](http://www.w3.org/2000/01/rdf-schema#comment) ""^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [BDS_subset](http://purl.obolibrary.org/obo/cl/cl-base#BDS_subset) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### Bergmann glial cell `http://purl.obolibrary.org/obo/CL_0000644` +#### Removed +- [Bergmann glial cell](http://purl.obolibrary.org/obo/CL_0000644) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009282"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Bergmann glial cell](http://purl.obolibrary.org/obo/CL_0000644) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009282"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532` +#### Removed +- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009243"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009243"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### CNS interneuron `http://purl.obolibrary.org/obo/CL_0000402` +#### Removed +- [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009191"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009191"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### CNS long range interneuron `http://purl.obolibrary.org/obo/CL_0000410` +#### Removed +- [CNS long range interneuron](http://purl.obolibrary.org/obo/CL_0000410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009195"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [CNS long range interneuron](http://purl.obolibrary.org/obo/CL_0000410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009195"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### CNS neuron (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000117` +#### Removed +- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009067"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009067"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### CNS short range interneuron `http://purl.obolibrary.org/obo/CL_0000406` +#### Removed +- [CNS short range interneuron](http://purl.obolibrary.org/obo/CL_0000406) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009194"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [CNS short range interneuron](http://purl.obolibrary.org/obo/CL_0000406) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009194"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Caenorhabditis hypodermal cell `http://purl.obolibrary.org/obo/CL_0000411` +#### Removed +- [Caenorhabditis hypodermal cell](http://purl.obolibrary.org/obo/CL_0000411) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009196"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Caenorhabditis hypodermal cell](http://purl.obolibrary.org/obo/CL_0000411) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009196"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Cajal-Retzius cell `http://purl.obolibrary.org/obo/CL_0000695` +#### Removed +- [Cajal-Retzius cell](http://purl.obolibrary.org/obo/CL_0000695) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009300"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Cajal-Retzius cell](http://purl.obolibrary.org/obo/CL_0000695) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009300"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### GABAergic neuron `http://purl.obolibrary.org/obo/CL_0000617` +#### Removed +- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007228"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009276"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007228"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009276"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### GO_0005903 `http://purl.obolibrary.org/obo/GO_0005903` + +#### Added +- Class: [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903) + + +### Hofbauer cell `http://purl.obolibrary.org/obo/CL_3000001` +#### Removed +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) + +#### Added +- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) + + +### Kenyon cell `http://purl.obolibrary.org/obo/CL_0000673` +#### Removed +- [Kenyon cell](http://purl.obolibrary.org/obo/CL_0000673) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003686"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Kenyon cell](http://purl.obolibrary.org/obo/CL_0000673) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003686"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Kolmer-Agduhr neuron `http://purl.obolibrary.org/obo/CL_0005007` +#### Removed +- [Kolmer-Agduhr neuron](http://purl.obolibrary.org/obo/CL_0005007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005240"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Kolmer-Agduhr neuron](http://purl.obolibrary.org/obo/CL_0005007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005240"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### L2 marginal neuron `http://purl.obolibrary.org/obo/CL_4042012` + +#### Added +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "layer 2 marginal neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32108571"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [label](http://www.w3.org/2000/01/rdf-schema#label) "L2 marginal neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [date](http://purl.org/dc/terms/date) "2024-04-23T09:31:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "L2MN"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042012"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "L2MN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29311847"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32108571"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29311847"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32108571"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) + +- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) SubClassOf [L2 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030060) + + +### Lamp5 Lhx6 neuron `http://purl.obolibrary.org/obo/CL_4042013` + +#### Added +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Ivy cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36007006"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042013"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Lamp5-Lhx6 type"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824669"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36007006"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34004146"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [date](http://purl.org/dc/terms/date) "2024-04-23T09:37:55Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [label](http://www.w3.org/2000/01/rdf-schema#label) "Lamp5 Lhx6 neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) + +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) + + +### Leydig cell `http://purl.obolibrary.org/obo/CL_0000178` +#### Removed +- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009108"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009108"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### M cell of gut `http://purl.obolibrary.org/obo/CL_0000682` +#### Removed +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009293"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009293"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Malpighian tubule stellate cell `http://purl.obolibrary.org/obo/CL_1000155` +#### Removed +- [Malpighian tubule stellate cell](http://purl.obolibrary.org/obo/CL_1000155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005797"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Malpighian tubule stellate cell](http://purl.obolibrary.org/obo/CL_1000155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005797"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Mauthner neuron `http://purl.obolibrary.org/obo/CL_0000246` +#### Removed +- [Mauthner neuron](http://purl.obolibrary.org/obo/CL_0000246) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009149"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Mauthner neuron](http://purl.obolibrary.org/obo/CL_0000246) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009149"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Merkel cell `http://purl.obolibrary.org/obo/CL_0000242` +#### Removed +- [Merkel cell](http://purl.obolibrary.org/obo/CL_0000242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009146"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Merkel cell](http://purl.obolibrary.org/obo/CL_0000242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009146"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Meynert cell `http://purl.obolibrary.org/obo/CL_2000056` +#### Removed +- [Meynert cell](http://purl.obolibrary.org/obo/CL_2000056) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [Meynert cell](http://purl.obolibrary.org/obo/CL_2000056) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### Mueller cell `http://purl.obolibrary.org/obo/CL_0000636` +#### Removed +- [Mueller cell](http://purl.obolibrary.org/obo/CL_0000636) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009280"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Mueller cell](http://purl.obolibrary.org/obo/CL_0000636) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009280"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### OFF-bipolar cell `http://purl.obolibrary.org/obo/CL_0000750` +#### Removed +- [OFF-bipolar cell](http://purl.obolibrary.org/obo/CL_0000750) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009320"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [OFF-bipolar cell](http://purl.obolibrary.org/obo/CL_0000750) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009320"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ON-bipolar cell `http://purl.obolibrary.org/obo/CL_0000749` +#### Removed +- [ON-bipolar cell](http://purl.obolibrary.org/obo/CL_0000749) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009319"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ON-bipolar cell](http://purl.obolibrary.org/obo/CL_0000749) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009319"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### PATO_0002064 `http://purl.obolibrary.org/obo/PATO_0002064` + +#### Added +- Class: [PATO_0002064](http://purl.obolibrary.org/obo/PATO_0002064) + + +### Purkinje cell `http://purl.obolibrary.org/obo/CL_0000121` +#### Removed +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009071"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009071"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R1 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000687` +#### Removed +- [R1 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004213"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R1 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004213"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R2 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000690` +#### Removed +- [R2 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000690) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004215"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R2 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000690) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004215"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R3 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000694` +#### Removed +- [R3 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000694) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004217"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R3 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000694) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004217"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R4 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000697` +#### Removed +- [R4 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000697) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R4 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000697) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R5 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000702` +#### Removed +- [R5 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000702) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R5 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000702) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R6 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000705` +#### Removed +- [R6 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000705) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004223"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R6 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000705) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004223"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R7 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000707` +#### Removed +- [R7 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004225"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R7 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004225"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### R8 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000709` +#### Removed +- [R8 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000709) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004227"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [R8 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000709) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004227"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Rohon-Beard neuron `http://purl.obolibrary.org/obo/CL_0000247` +#### Removed +- [Rohon-Beard neuron](http://purl.obolibrary.org/obo/CL_0000247) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009150"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Rohon-Beard neuron](http://purl.obolibrary.org/obo/CL_0000247) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009150"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Schwann cell precursor `http://purl.obolibrary.org/obo/CL_0002375` +#### Removed +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### Sertoli cell `http://purl.obolibrary.org/obo/CL_0000216` +#### Removed +- [Sertoli cell](http://purl.obolibrary.org/obo/CL_0000216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009133"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [Sertoli cell](http://purl.obolibrary.org/obo/CL_0000216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009133"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### T cell `http://purl.obolibrary.org/obo/CL_0000084` +#### Removed +- [T cell](http://purl.obolibrary.org/obo/CL_0000084) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009046"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [T cell](http://purl.obolibrary.org/obo/CL_0000084) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009046"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### UBERON_0000065 `http://purl.obolibrary.org/obo/UBERON_0000065` +#### Removed +- Class: [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065) + + + +### UBERON_0001557 `http://purl.obolibrary.org/obo/UBERON_0001557` +#### Removed +- Class: [UBERON_0001557](http://purl.obolibrary.org/obo/UBERON_0001557) + + + +### UBERON_0001558 `http://purl.obolibrary.org/obo/UBERON_0001558` +#### Removed +- Class: [UBERON_0001558](http://purl.obolibrary.org/obo/UBERON_0001558) + + + +### UBERON_0002051 `http://purl.obolibrary.org/obo/UBERON_0002051` + +#### Added +- Class: [UBERON_0002051](http://purl.obolibrary.org/obo/UBERON_0002051) + + +### UBERON_0004196 `http://purl.obolibrary.org/obo/UBERON_0004196` + +#### Added +- Class: [UBERON_0004196](http://purl.obolibrary.org/obo/UBERON_0004196) + + +### UBERON_0004197 `http://purl.obolibrary.org/obo/UBERON_0004197` + +#### Added +- Class: [UBERON_0004197](http://purl.obolibrary.org/obo/UBERON_0004197) + + +### UBERON_0004814 `http://purl.obolibrary.org/obo/UBERON_0004814` + +#### Added +- Class: [UBERON_0004814](http://purl.obolibrary.org/obo/UBERON_0004814) + + +### UBERON_0004815 `http://purl.obolibrary.org/obo/UBERON_0004815` + +#### Added +- Class: [UBERON_0004815](http://purl.obolibrary.org/obo/UBERON_0004815) + + +### UBERON_0004903 `http://purl.obolibrary.org/obo/UBERON_0004903` + +#### Added +- Class: [UBERON_0004903](http://purl.obolibrary.org/obo/UBERON_0004903) + + +### UBERON_0008397 `http://purl.obolibrary.org/obo/UBERON_0008397` + +#### Added +- Class: [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397) + + +### UV sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000494` +#### Removed +- [UV sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000494) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [UV sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000494) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### absorptive cell `http://purl.obolibrary.org/obo/CL_0000212` +#### Removed +- [absorptive cell](http://purl.obolibrary.org/obo/CL_0000212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009129"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [absorptive cell](http://purl.obolibrary.org/obo/CL_0000212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009129"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### acinar cell `http://purl.obolibrary.org/obo/CL_0000622` +#### Removed +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009277"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009277"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### adaxial cell `http://purl.obolibrary.org/obo/CL_0007016` +#### Removed +- [adaxial cell](http://purl.obolibrary.org/obo/CL_0007016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000003"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [adaxial cell](http://purl.obolibrary.org/obo/CL_0007016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000003"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### added_for_HCA `http://purl.obolibrary.org/obo/cl/cl-base#added_for_HCA` + +#### Added +- [added_for_HCA](http://purl.obolibrary.org/obo/cl/cl-base#added_for_HCA) [comment](http://www.w3.org/2000/01/rdf-schema#comment) ""^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [added_for_HCA](http://purl.obolibrary.org/obo/cl/cl-base#added_for_HCA) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### adepithelial cell `http://purl.obolibrary.org/obo/CL_0000462` +#### Removed +- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### adipocyte `http://purl.obolibrary.org/obo/CL_0000136` +#### Removed +- [adipocyte](http://purl.obolibrary.org/obo/CL_0000136) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009082"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [adipocyte](http://purl.obolibrary.org/obo/CL_0000136) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009082"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### adipose microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000072` +#### Removed +- [adipose microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000072) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [adipose microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000072) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### adrenal medulla chromaffin cell `http://purl.obolibrary.org/obo/CL_0000336` +#### Removed +- [adrenal medulla chromaffin cell](http://purl.obolibrary.org/obo/CL_0000336) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009167"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [adrenal medulla chromaffin cell](http://purl.obolibrary.org/obo/CL_0000336) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009167"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### adrenergic neuron `http://purl.obolibrary.org/obo/CL_0000109` +#### Removed +- [adrenergic neuron](http://purl.obolibrary.org/obo/CL_0000109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009061"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [adrenergic neuron](http://purl.obolibrary.org/obo/CL_0000109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009061"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### adrenocorticotropic hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000467` +#### Removed +- [adrenocorticotropic hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009216"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [adrenocorticotropic hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009216"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### afferent neuron `http://purl.obolibrary.org/obo/CL_0000526` +#### Removed +- [afferent neuron](http://purl.obolibrary.org/obo/CL_0000526) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009238"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [afferent neuron](http://purl.obolibrary.org/obo/CL_0000526) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009238"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### alkali secreting cell `http://purl.obolibrary.org/obo/CL_0000435` +#### Removed +- [alkali secreting cell](http://purl.obolibrary.org/obo/CL_0000435) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009201"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [alkali secreting cell](http://purl.obolibrary.org/obo/CL_0000435) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009201"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000789` +#### Removed +- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009335"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009335"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### alveolar capillary type 1 endothelial cell `http://purl.obolibrary.org/obo/CL_4028002` +#### Removed +- [alveolar capillary type 1 endothelial cell](http://purl.obolibrary.org/obo/CL_4028002) SubClassOf [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) + +#### Added +- [alveolar capillary type 1 endothelial cell](http://purl.obolibrary.org/obo/CL_4028002) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) + + +### alveolar capillary type 2 endothelial cell `http://purl.obolibrary.org/obo/CL_4028003` +#### Removed +- [alveolar capillary type 2 endothelial cell](http://purl.obolibrary.org/obo/CL_4028003) SubClassOf [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) + +#### Added +- [alveolar capillary type 2 endothelial cell](http://purl.obolibrary.org/obo/CL_4028003) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) + + +### alveolar type 2 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028006` +#### Removed +- [alveolar type 2 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028006) [label](http://www.w3.org/2000/01/rdf-schema#label) "alveolar type 2 fibroblast cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [alveolar type 2 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "AdvF"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33208946"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [alveolar type 2 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "alveolar type 2 fibroblast cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [alveolar type 2 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028006) [label](http://www.w3.org/2000/01/rdf-schema#label) "alveolar adventitial fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### amacrine cell `http://purl.obolibrary.org/obo/CL_0000561` +#### Removed +- [amacrine cell](http://purl.obolibrary.org/obo/CL_0000561) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009255"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [amacrine cell](http://purl.obolibrary.org/obo/CL_0000561) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009255"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### androgen secreting cell `http://purl.obolibrary.org/obo/CL_0000593` +#### Removed +- [androgen secreting cell](http://purl.obolibrary.org/obo/CL_0000593) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009271"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [androgen secreting cell](http://purl.obolibrary.org/obo/CL_0000593) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009271"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### angioblastic mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000566` +#### Removed +- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009258"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009258"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### anterior horn motor neuron `http://purl.obolibrary.org/obo/CL_2000048` +#### Removed +- [anterior horn motor neuron](http://purl.obolibrary.org/obo/CL_2000048) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [anterior horn motor neuron](http://purl.obolibrary.org/obo/CL_2000048) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### anterior lateral line neuromast hair cell `http://purl.obolibrary.org/obo/CL_2000034` +#### Removed +- [anterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000034) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [anterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000034) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### anterior lateral line neuromast mantle cell `http://purl.obolibrary.org/obo/CL_2000035` +#### Removed +- [anterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000035) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [anterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000035) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### anterior lateral line neuromast supporting cell `http://purl.obolibrary.org/obo/CL_2000036` +#### Removed +- [anterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000036) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [anterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000036) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### anterior visceral endoderm cell `http://purl.obolibrary.org/obo/CL_2000075` +#### Removed +- [anterior visceral endoderm cell](http://purl.obolibrary.org/obo/CL_2000075) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [anterior visceral endoderm cell](http://purl.obolibrary.org/obo/CL_2000075) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### articular chondrocyte of knee joint `http://purl.obolibrary.org/obo/CL_2000007` +#### Removed +- [articular chondrocyte of knee joint](http://purl.obolibrary.org/obo/CL_2000007) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [articular chondrocyte of knee joint](http://purl.obolibrary.org/obo/CL_2000007) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### astrocyte `http://purl.obolibrary.org/obo/CL_0000127` +#### Removed +- [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009075"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009075"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### auditory epithelial supporting cell `http://purl.obolibrary.org/obo/CL_0005014` +#### Removed +- [auditory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0005014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005244"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [auditory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0005014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005244"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### auditory hair cell `http://purl.obolibrary.org/obo/CL_0000202` +#### Removed +- [auditory hair cell](http://purl.obolibrary.org/obo/CL_0000202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009121"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [auditory hair cell](http://purl.obolibrary.org/obo/CL_0000202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009121"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### autonomic neuron `http://purl.obolibrary.org/obo/CL_0000107` +#### Removed +- [autonomic neuron](http://purl.obolibrary.org/obo/CL_0000107) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009059"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [autonomic neuron](http://purl.obolibrary.org/obo/CL_0000107) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009059"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### band form neutrophil `http://purl.obolibrary.org/obo/CL_0000560` +#### Removed +- [band form neutrophil](http://purl.obolibrary.org/obo/CL_0000560) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009254"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [band form neutrophil](http://purl.obolibrary.org/obo/CL_0000560) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009254"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### barrier cell `http://purl.obolibrary.org/obo/CL_0000215` +#### Removed +- [barrier cell](http://purl.obolibrary.org/obo/CL_0000215) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009132"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [barrier cell](http://purl.obolibrary.org/obo/CL_0000215) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009132"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### basal cell of epithelium of lobular bronchiole `http://purl.obolibrary.org/obo/CL_1000352` +#### Removed +- [basal cell of epithelium of lobular bronchiole](http://purl.obolibrary.org/obo/CL_1000352) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) + +- [basal cell of epithelium of lobular bronchiole](http://purl.obolibrary.org/obo/CL_1000352) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + + +### basal cell of epithelium of respiratory bronchiole `http://purl.obolibrary.org/obo/CL_1000351` +#### Removed +- [basal cell of epithelium of respiratory bronchiole](http://purl.obolibrary.org/obo/CL_1000351) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) + +- [basal cell of epithelium of respiratory bronchiole](http://purl.obolibrary.org/obo/CL_1000351) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + + +### basal cell of epithelium of terminal bronchiole `http://purl.obolibrary.org/obo/CL_1000350` +#### Removed +- [basal cell of epithelium of terminal bronchiole](http://purl.obolibrary.org/obo/CL_1000350) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + +- [basal cell of epithelium of terminal bronchiole](http://purl.obolibrary.org/obo/CL_1000350) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) + + + +### basal cell of epithelium of trachea `http://purl.obolibrary.org/obo/CL_1000348` +#### Removed +- [basal cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000348) SubClassOf [tracheal epithelial cell](http://purl.obolibrary.org/obo/CL_0000307) + + + +### basal cell of olfactory epithelium `http://purl.obolibrary.org/obo/CL_0002169` + +#### Added +- [basal cell of olfactory epithelium](http://purl.obolibrary.org/obo/CL_0002169) SubClassOf [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) + + +### basket cell `http://purl.obolibrary.org/obo/CL_0000118` +#### Removed +- [basket cell](http://purl.obolibrary.org/obo/CL_0000118) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009068"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [basket cell](http://purl.obolibrary.org/obo/CL_0000118) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009068"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### basophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000549` +#### Removed +- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005236"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005236"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### biogenic amine secreting cell `http://purl.obolibrary.org/obo/CL_0000457` +#### Removed +- [biogenic amine secreting cell](http://purl.obolibrary.org/obo/CL_0000457) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009212"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [biogenic amine secreting cell](http://purl.obolibrary.org/obo/CL_0000457) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009212"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### bipolar neuron `http://purl.obolibrary.org/obo/CL_0000103` +#### Removed +- [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009055"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009055"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### bladder microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000040` +#### Removed +- [bladder microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000040) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [bladder microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000040) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### blastemal cell `http://purl.obolibrary.org/obo/CL_0000354` +#### Removed +- [blastemal cell](http://purl.obolibrary.org/obo/CL_0000354) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009178"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [blastemal cell](http://purl.obolibrary.org/obo/CL_0000354) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009178"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### blastoderm cell `http://purl.obolibrary.org/obo/CL_0000353` +#### Removed +- [blastoderm cell](http://purl.obolibrary.org/obo/CL_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009177"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [blastoderm cell](http://purl.obolibrary.org/obo/CL_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009177"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### blood cell `http://purl.obolibrary.org/obo/CL_0000081` +#### Removed +- [blood cell](http://purl.obolibrary.org/obo/CL_0000081) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009044"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [blood cell](http://purl.obolibrary.org/obo/CL_0000081) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009044"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0000071` +#### Removed +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cuboidal endothelial cell of vascular tree"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009036"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) EquivalentTo [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004638](http://purl.obolibrary.org/obo/UBERON_0004638)) + +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009036"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001981](http://purl.obolibrary.org/obo/UBERON_0001981)) + + +### blood_and_immune_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#blood_and_immune_upper_slim` + +#### Added +- [blood_and_immune_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#blood_and_immune_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [blood_and_immune_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#blood_and_immune_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### blue sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000495` +#### Removed +- [blue sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000495) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009222"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [blue sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000495) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009222"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### border follicle cell `http://purl.obolibrary.org/obo/CL_0000579` +#### Removed +- [border follicle cell](http://purl.obolibrary.org/obo/CL_0000579) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004905"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [border follicle cell](http://purl.obolibrary.org/obo/CL_0000579) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004905"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### brain macroglial cell `http://purl.obolibrary.org/obo/CL_2000005` +#### Removed +- [brain macroglial cell](http://purl.obolibrary.org/obo/CL_2000005) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [brain macroglial cell](http://purl.obolibrary.org/obo/CL_2000005) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### brain microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000044` +#### Removed +- [brain microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000044) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [brain microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000044) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### brain pericyte `http://purl.obolibrary.org/obo/CL_2000043` +#### Removed +- [brain pericyte](http://purl.obolibrary.org/obo/CL_2000043) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [brain pericyte](http://purl.obolibrary.org/obo/CL_2000043) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### brainstem motor neuron `http://purl.obolibrary.org/obo/CL_2000047` +#### Removed +- [brainstem motor neuron](http://purl.obolibrary.org/obo/CL_2000047) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [brainstem motor neuron](http://purl.obolibrary.org/obo/CL_2000047) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### branchiomotor neuron `http://purl.obolibrary.org/obo/CL_0005023` +#### Removed +- [branchiomotor neuron](http://purl.obolibrary.org/obo/CL_0005023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005731"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [branchiomotor neuron](http://purl.obolibrary.org/obo/CL_0005023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005731"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### bronchioalveolar stem cell `http://purl.obolibrary.org/obo/CL_0002638` +#### Removed +- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) EquivalentTo [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001955](http://purl.obolibrary.org/obo/UBERON_0001955)) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001958](http://purl.obolibrary.org/obo/UBERON_0001958)) + +- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [basal cell of epithelium of terminal bronchiole](http://purl.obolibrary.org/obo/CL_1000350) + +- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [basal cell of epithelium of respiratory bronchiole](http://purl.obolibrary.org/obo/CL_1000351) + +#### Added +- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002051](http://purl.obolibrary.org/obo/UBERON_0002051) + +- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004903](http://purl.obolibrary.org/obo/UBERON_0004903) + +- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### bronchus fibroblast of lung `http://purl.obolibrary.org/obo/CL_2000093` +#### Removed +- [bronchus fibroblast of lung](http://purl.obolibrary.org/obo/CL_2000093) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [bronchus fibroblast of lung](http://purl.obolibrary.org/obo/CL_2000093) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### brush border cell of the proximal tubule `http://purl.obolibrary.org/obo/CL_0002307` +#### Removed +- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:1-4160-2328-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:1-4160-2328-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) EquivalentTo [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + +- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) SubClassOf [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) + + +### brush border epithelial cell `http://purl.obolibrary.org/obo/CL_0000239` +#### Removed +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009143"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) + +#### Added +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25422372"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1152/ajpgi.00005.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009143"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + +- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903) + + +### brush cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002075` +#### Removed +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) EquivalentTo [brush cell](http://purl.obolibrary.org/obo/CL_0002204) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196)) + +#### Added +- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) EquivalentTo [brush cell](http://purl.obolibrary.org/obo/CL_0002204) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) + + +### calcitonin secreting cell `http://purl.obolibrary.org/obo/CL_0000443` +#### Removed +- [calcitonin secreting cell](http://purl.obolibrary.org/obo/CL_0000443) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009206"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [calcitonin secreting cell](http://purl.obolibrary.org/obo/CL_0000443) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009206"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### calvarial osteoblast `http://purl.obolibrary.org/obo/CL_2000058` +#### Removed +- [calvarial osteoblast](http://purl.obolibrary.org/obo/CL_2000058) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [calvarial osteoblast](http://purl.obolibrary.org/obo/CL_2000058) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### capillary endothelial cell `http://purl.obolibrary.org/obo/CL_0002144` + +#### Added +- [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) SubClassOf [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) + + +### cardiac atrium fibroblast `http://purl.obolibrary.org/obo/CL_2000067` +#### Removed +- [cardiac atrium fibroblast](http://purl.obolibrary.org/obo/CL_2000067) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [cardiac atrium fibroblast](http://purl.obolibrary.org/obo/CL_2000067) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### cardiac mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000569` +#### Removed +- [cardiac mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000569) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009259"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cardiac mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000569) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009259"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cardiac muscle cell `http://purl.obolibrary.org/obo/CL_0000746` +#### Removed +- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009316"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009316"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cardiac muscle myoblast `http://purl.obolibrary.org/obo/CL_0000513` +#### Removed +- [cardiac muscle myoblast](http://purl.obolibrary.org/obo/CL_0000513) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009234"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cardiac muscle myoblast](http://purl.obolibrary.org/obo/CL_0000513) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009234"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cardiac septum cell `http://purl.obolibrary.org/obo/CL_2000022` +#### Removed +- [cardiac septum cell](http://purl.obolibrary.org/obo/CL_2000022) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [cardiac septum cell](http://purl.obolibrary.org/obo/CL_2000022) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### cardiac valve cell `http://purl.obolibrary.org/obo/CL_1000147` +#### Removed +- [cardiac valve cell](http://purl.obolibrary.org/obo/CL_1000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009402"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cardiac valve cell](http://purl.obolibrary.org/obo/CL_1000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009402"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cardiac ventricle fibroblast `http://purl.obolibrary.org/obo/CL_2000066` +#### Removed +- [cardiac ventricle fibroblast](http://purl.obolibrary.org/obo/CL_2000066) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [cardiac ventricle fibroblast](http://purl.obolibrary.org/obo/CL_2000066) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### cardioblast (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000465` +#### Removed +- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001666"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001666"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### caudal ganglionic eminence derived GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023070` +#### Removed +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [UBERON_0004026](http://purl.obolibrary.org/obo/UBERON_0004026)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) + +#### Added +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) [2374](https://github.com/obophenotype/cell-ontology/pull/2374) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "caudal ganglionic eminence derived GABAergic interneuron +and caudal ganglionic eminence derived interneuron are the same cell type. +The two must be merged and one needs to be defined as obsolete. +We decided to deprecate the entity with the more specific term and redundant qualities +in the label. See comments in issue 2357."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete caudal ganglionic eminence derived GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### caudal ganglionic eminence derived interneuron `http://purl.obolibrary.org/obo/CL_4023064` +#### Removed +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An interneuron that is derived from the caudal ganglionic eminence."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2022.10.12.511898"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) + +#### Added +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE-derived interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "caudal ganglionic eminence derived GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE-derived cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27034423"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE-derived GABAergic IN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27034423"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An interneuron that is derived from the caudal ganglionic eminence."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + + +### cell `http://purl.obolibrary.org/obo/CL_0000000` +#### Removed +- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007002"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009000"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007002"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009000"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cell of skeletal muscle `http://purl.obolibrary.org/obo/CL_0000188` +#### Removed +- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009115"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009115"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cementoblast `http://purl.obolibrary.org/obo/CL_0000061` +#### Removed +- [cementoblast](http://purl.obolibrary.org/obo/CL_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009030"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cementoblast](http://purl.obolibrary.org/obo/CL_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009030"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cementocyte `http://purl.obolibrary.org/obo/CL_0000141` +#### Removed +- [cementocyte](http://purl.obolibrary.org/obo/CL_0000141) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009087"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cementocyte](http://purl.obolibrary.org/obo/CL_0000141) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009087"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### central nervous system neuron `http://purl.obolibrary.org/obo/CL_2000029` +#### Removed +- [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### centripetally migrating follicle cell `http://purl.obolibrary.org/obo/CL_0000671` +#### Removed +- [centripetally migrating follicle cell](http://purl.obolibrary.org/obo/CL_0000671) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004906"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [centripetally migrating follicle cell](http://purl.obolibrary.org/obo/CL_0000671) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004906"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cerebellar Golgi cell `http://purl.obolibrary.org/obo/CL_0000119` +#### Removed +- [cerebellar Golgi cell](http://purl.obolibrary.org/obo/CL_0000119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009069"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cerebellar Golgi cell](http://purl.obolibrary.org/obo/CL_0000119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009069"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cerebellar granule cell `http://purl.obolibrary.org/obo/CL_0001031` +#### Removed +- [cerebellar granule cell](http://purl.obolibrary.org/obo/CL_0001031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001691"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cerebellar granule cell](http://purl.obolibrary.org/obo/CL_0001031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001691"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cerebellum basket cell `http://purl.obolibrary.org/obo/CL_2000027` +#### Removed +- [cerebellum basket cell](http://purl.obolibrary.org/obo/CL_2000027) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [cerebellum basket cell](http://purl.obolibrary.org/obo/CL_2000027) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### cerebellum glutamatergic neuron `http://purl.obolibrary.org/obo/CL_2000028` +#### Removed +- [cerebellum glutamatergic neuron](http://purl.obolibrary.org/obo/CL_2000028) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [cerebellum glutamatergic neuron](http://purl.obolibrary.org/obo/CL_2000028) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### cerebrospinal fluid secreting cell `http://purl.obolibrary.org/obo/CL_0000686` +#### Removed +- [cerebrospinal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000686) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009295"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cerebrospinal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000686) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009295"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### chemoreceptor cell `http://purl.obolibrary.org/obo/CL_0000206` +#### Removed +- [chemoreceptor cell](http://purl.obolibrary.org/obo/CL_0000206) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009124"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [chemoreceptor cell](http://purl.obolibrary.org/obo/CL_0000206) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009124"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cholangiocyte `http://purl.obolibrary.org/obo/CL_1000488` +#### Removed +- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009397"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009397"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cholinergic neuron `http://purl.obolibrary.org/obo/CL_0000108` +#### Removed +- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007173"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009060"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009060"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007173"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### chondroblast `http://purl.obolibrary.org/obo/CL_0000058` +#### Removed +- [chondroblast](http://purl.obolibrary.org/obo/CL_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009027"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [chondroblast](http://purl.obolibrary.org/obo/CL_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009027"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### chondrocyte `http://purl.obolibrary.org/obo/CL_0000138` +#### Removed +- [chondrocyte](http://purl.obolibrary.org/obo/CL_0000138) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [chondrocyte](http://purl.obolibrary.org/obo/CL_0000138) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### chorionic girdle cell `http://purl.obolibrary.org/obo/CL_4040001` +#### Removed +- [chorionic girdle cell](http://purl.obolibrary.org/obo/CL_4040001) [note](http://purl.obolibrary.org/obo/cl/cl-base#note) "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27280409"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [chorionic girdle cell](http://purl.obolibrary.org/obo/CL_4040001) [note](http://www.geneontology.org/formats/oboInOwl#note) "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27280409"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### choroid plexus epithelial cell `http://purl.obolibrary.org/obo/CL_0000706` +#### Removed +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009304"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009304"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### choroidal cell of the eye `http://purl.obolibrary.org/obo/CL_0000348` +#### Removed +- [choroidal cell of the eye](http://purl.obolibrary.org/obo/CL_0000348) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009175"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [choroidal cell of the eye](http://purl.obolibrary.org/obo/CL_0000348) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009175"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### chromaffin cell `http://purl.obolibrary.org/obo/CL_0000166` +#### Removed +- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009099"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009099"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ciliated cell `http://purl.obolibrary.org/obo/CL_0000064` +#### Removed +- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009032"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009032"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0000067` +#### Removed +- [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009035"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009035"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ciliated epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_3000000` +#### Removed +- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) + +#### Added +- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) + + +### ciliated olfactory receptor neuron `http://purl.obolibrary.org/obo/CL_0000847` +#### Removed +- [ciliated olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000847) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009358"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ciliated olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000847) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009358"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### circulating cell `http://purl.obolibrary.org/obo/CL_0000080` +#### Removed +- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009043"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009043"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### collagen secreting cell `http://purl.obolibrary.org/obo/CL_0000667` +#### Removed +- [collagen secreting cell](http://purl.obolibrary.org/obo/CL_0000667) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009287"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [collagen secreting cell](http://purl.obolibrary.org/obo/CL_0000667) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009287"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### colon endothelial cell `http://purl.obolibrary.org/obo/CL_1001572` +#### Removed +- [colon endothelial cell](http://purl.obolibrary.org/obo/CL_1001572) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) + + + +### columnar chondrocyte `http://purl.obolibrary.org/obo/CL_0000744` +#### Removed +- [columnar chondrocyte](http://purl.obolibrary.org/obo/CL_0000744) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009314"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [columnar chondrocyte](http://purl.obolibrary.org/obo/CL_0000744) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009314"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### columnar/cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000075` +#### Removed +- [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009038"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009038"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### committed double negative thymocyte (Homo sapiens) `http://purl.obolibrary.org/obo/CL_0009082` + +#### Added +- [committed double negative thymocyte (Homo sapiens)](http://purl.obolibrary.org/obo/CL_0009082) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + + +### common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0000051` +#### Removed +- [common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000051) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009023"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000051) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009023"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### common myeloid progenitor `http://purl.obolibrary.org/obo/CL_0000049` +#### Removed +- [common myeloid progenitor](http://purl.obolibrary.org/obo/CL_0000049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009021"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [common myeloid progenitor](http://purl.obolibrary.org/obo/CL_0000049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009021"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### compound eye cone cell `http://purl.obolibrary.org/obo/CL_0000718` +#### Removed +- [compound eye cone cell](http://purl.obolibrary.org/obo/CL_0000718) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004193"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [compound eye cone cell](http://purl.obolibrary.org/obo/CL_0000718) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004193"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### compound eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_2000019` +#### Removed +- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00006009"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00006009"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### cone retinal bipolar cell `http://purl.obolibrary.org/obo/CL_0000752` +#### Removed +- [cone retinal bipolar cell](http://purl.obolibrary.org/obo/CL_0000752) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009322"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cone retinal bipolar cell](http://purl.obolibrary.org/obo/CL_0000752) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009322"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### conjunctiva goblet cell `http://purl.obolibrary.org/obo/CL_2000084` +#### Removed +- [conjunctiva goblet cell](http://purl.obolibrary.org/obo/CL_2000084) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [conjunctiva goblet cell](http://purl.obolibrary.org/obo/CL_2000084) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### connective tissue cell `http://purl.obolibrary.org/obo/CL_0002320` +#### Removed +- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009392"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009392"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cord blood hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_2000095` +#### Removed +- [cord blood hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_2000095) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [cord blood hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_2000095) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### corneal endothelial cell `http://purl.obolibrary.org/obo/CL_0000132` +#### Removed +- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009079"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) SubClassOf [neurecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0000710) + +#### Added +- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009079"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### corneal epithelial cell `http://purl.obolibrary.org/obo/CL_0000575` +#### Removed +- [corneal epithelial cell](http://purl.obolibrary.org/obo/CL_0000575) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009264"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [corneal epithelial cell](http://purl.obolibrary.org/obo/CL_0000575) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009264"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cranial motor neuron `http://purl.obolibrary.org/obo/CL_0015000` +#### Removed +- [cranial motor neuron](http://purl.obolibrary.org/obo/CL_0015000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005730"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cranial motor neuron](http://purl.obolibrary.org/obo/CL_0015000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005730"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### crypt olfactory receptor neuron `http://purl.obolibrary.org/obo/CL_0000849` +#### Removed +- [crypt olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000849) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009360"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [crypt olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000849) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009360"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cyanoblast `http://purl.obolibrary.org/obo/CL_0005005` +#### Removed +- [cyanoblast](http://purl.obolibrary.org/obo/CL_0005005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005332"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cyanoblast](http://purl.obolibrary.org/obo/CL_0005005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005332"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### cyanophore `http://purl.obolibrary.org/obo/CL_0000747` +#### Removed +- [cyanophore](http://purl.obolibrary.org/obo/CL_0000747) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009317"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [cyanophore](http://purl.obolibrary.org/obo/CL_0000747) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009317"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### dendritic cell `http://purl.obolibrary.org/obo/CL_0000451` +#### Removed +- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009209"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009209"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### dental papilla cell `http://purl.obolibrary.org/obo/CL_0000345` +#### Removed +- [dental papilla cell](http://purl.obolibrary.org/obo/CL_0000345) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009173"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [dental papilla cell](http://purl.obolibrary.org/obo/CL_0000345) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009173"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### dentate gyrus granule cell `http://purl.obolibrary.org/obo/CL_2000089` +#### Removed +- [dentate gyrus granule cell](http://purl.obolibrary.org/obo/CL_2000089) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [dentate gyrus granule cell](http://purl.obolibrary.org/obo/CL_2000089) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### dentate gyrus of hippocampal formation basket cell `http://purl.obolibrary.org/obo/CL_2000087` +#### Removed +- [dentate gyrus of hippocampal formation basket cell](http://purl.obolibrary.org/obo/CL_2000087) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [dentate gyrus of hippocampal formation basket cell](http://purl.obolibrary.org/obo/CL_2000087) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### dentate gyrus of hippocampal formation stellate cell `http://purl.obolibrary.org/obo/CL_2000090` +#### Removed +- [dentate gyrus of hippocampal formation stellate cell](http://purl.obolibrary.org/obo/CL_2000090) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [dentate gyrus of hippocampal formation stellate cell](http://purl.obolibrary.org/obo/CL_2000090) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### dermis blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000010` +#### Removed +- [dermis blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000010) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [dermis blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000010) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### dermis lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000011` +#### Removed +- [dermis lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000011) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [dermis lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000011) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### dermis microvascular lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000041` +#### Removed +- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008339](http://purl.obolibrary.org/obo/UBERON_0008339) + +#### Added +- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + +- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) SubClassOf [dermal microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_0011030) + + +### deuterosomal cell `http://purl.obolibrary.org/obo/CL_4033044` +#### Removed +- [deuterosomal cell](http://purl.obolibrary.org/obo/CL_4033044) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + + + +### digestive enzyme secreting cell `http://purl.obolibrary.org/obo/CL_0000470` +#### Removed +- [digestive enzyme secreting cell](http://purl.obolibrary.org/obo/CL_0000470) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009217"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [digestive enzyme secreting cell](http://purl.obolibrary.org/obo/CL_0000470) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009217"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### dopaminergic neuron `http://purl.obolibrary.org/obo/CL_0000700` +#### Removed +- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009301"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009301"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### duct epithelial cell `http://purl.obolibrary.org/obo/CL_0000068` +#### Removed +- [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009372"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009372"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### early embryonic cell (metazoa) `http://purl.obolibrary.org/obo/CL_0000007` +#### Removed +- [early embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0000007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009002"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [early embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0000007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009002"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ecto-epithelial cell `http://purl.obolibrary.org/obo/CL_0002077` +#### Removed +- [ecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0002077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009385"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0002077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009385"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ectodermal cell `http://purl.obolibrary.org/obo/CL_0000221` +#### Removed +- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009137"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009137"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### efferent neuron `http://purl.obolibrary.org/obo/CL_0000527` +#### Removed +- [efferent neuron](http://purl.obolibrary.org/obo/CL_0000527) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009239"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [efferent neuron](http://purl.obolibrary.org/obo/CL_0000527) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009239"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### egg cell `http://purl.obolibrary.org/obo/CL_0000025` +#### Removed +- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00057012"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001570"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00057012"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001570"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### electrically active cell `http://purl.obolibrary.org/obo/CL_0000211` +#### Removed +- [electrically active cell](http://purl.obolibrary.org/obo/CL_0000211) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009128"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [electrically active cell](http://purl.obolibrary.org/obo/CL_0000211) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009128"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### electrically responsive cell `http://purl.obolibrary.org/obo/CL_0000393` +#### Removed +- [electrically responsive cell](http://purl.obolibrary.org/obo/CL_0000393) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009190"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [electrically responsive cell](http://purl.obolibrary.org/obo/CL_0000393) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009190"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### electrically signaling cell `http://purl.obolibrary.org/obo/CL_0000404` +#### Removed +- [electrically signaling cell](http://purl.obolibrary.org/obo/CL_0000404) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009193"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [electrically signaling cell](http://purl.obolibrary.org/obo/CL_0000404) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009193"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### embryonic blood vessel endothelial progenitor cell `http://purl.obolibrary.org/obo/CL_0002546` +#### Removed +- [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005773"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005773"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### embryonic cell (metazoa) `http://purl.obolibrary.org/obo/CL_0002321` +#### Removed +- [embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0002321) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007089"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0002321) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007089"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### embryonic crystal cell `http://purl.obolibrary.org/obo/CL_0000715` +#### Removed +- [embryonic crystal cell](http://purl.obolibrary.org/obo/CL_0000715) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001690"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [embryonic crystal cell](http://purl.obolibrary.org/obo/CL_0000715) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001690"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### embryonic fibroblast `http://purl.obolibrary.org/obo/CL_2000042` +#### Removed +- [embryonic fibroblast](http://purl.obolibrary.org/obo/CL_2000042) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [embryonic fibroblast](http://purl.obolibrary.org/obo/CL_2000042) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### embryonic gland hemocyte `http://purl.obolibrary.org/obo/CL_0000736` +#### Removed +- [embryonic gland hemocyte](http://purl.obolibrary.org/obo/CL_0000736) [label](http://www.w3.org/2000/01/rdf-schema#label) "embryonic gland hemocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [embryonic gland hemocyte](http://purl.obolibrary.org/obo/CL_0000736) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete embryonic gland hemocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endo-epithelial cell `http://purl.obolibrary.org/obo/CL_0002076` +#### Removed +- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009383"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009383"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223)) + + +### endocrine cell `http://purl.obolibrary.org/obo/CL_0000163` +#### Removed +- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009096"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009096"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endodermal cell `http://purl.obolibrary.org/obo/CL_0000223` +#### Removed +- [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009139"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009139"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endometrial microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000091` +#### Removed +- [endometrial microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000091) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [endometrial microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000091) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### endorphin secreting cell `http://purl.obolibrary.org/obo/CL_0000507` +#### Removed +- [endorphin secreting cell](http://purl.obolibrary.org/obo/CL_0000507) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009232"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endorphin secreting cell](http://purl.obolibrary.org/obo/CL_0000507) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009232"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### endothelial cell `http://purl.obolibrary.org/obo/CL_0000115` +#### Removed +- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009065"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) + +#### Added +- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009065"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) + +- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + + +### endothelial cell of Peyer's patch `http://purl.obolibrary.org/obo/CL_1000411` +#### Removed +- [endothelial cell of Peyer's patch](http://purl.obolibrary.org/obo/CL_1000411) SubClassOf [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) + + + +### endothelial cell of central vein of liver `http://purl.obolibrary.org/obo/CL_4033061` +#### Removed +- [endothelial cell of central vein of liver](http://purl.obolibrary.org/obo/CL_4033061) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +#### Added +- [endothelial cell of central vein of liver](http://purl.obolibrary.org/obo/CL_4033061) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) + + +### endothelial cell of coronary artery `http://purl.obolibrary.org/obo/CL_2000018` +#### Removed +- [endothelial cell of coronary artery](http://purl.obolibrary.org/obo/CL_2000018) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [endothelial cell of coronary artery](http://purl.obolibrary.org/obo/CL_2000018) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### endothelial cell of efferent lymphatic vessel `http://purl.obolibrary.org/obo/CL_4033006` +#### Removed +- [endothelial cell of efferent lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033006) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +#### Added +- [endothelial cell of efferent lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033006) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + +### endothelial cell of hepatic portal vein `http://purl.obolibrary.org/obo/CL_0009094` +#### Removed +- [endothelial cell of hepatic portal vein](http://purl.obolibrary.org/obo/CL_0009094) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +#### Added +- [endothelial cell of hepatic portal vein](http://purl.obolibrary.org/obo/CL_0009094) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) + + +### endothelial cell of hepatic sinusoid `http://purl.obolibrary.org/obo/CL_1000398` + +#### Added +- [endothelial cell of hepatic sinusoid](http://purl.obolibrary.org/obo/CL_1000398) SubClassOf [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) + + +### endothelial cell of high endothelial venule `http://purl.obolibrary.org/obo/CL_0002652` +#### Removed +- [endothelial cell of high endothelial venule](http://purl.obolibrary.org/obo/CL_0002652) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410037](http://purl.obolibrary.org/obo/UBERON_8410037)) + +- [endothelial cell of high endothelial venule](http://purl.obolibrary.org/obo/CL_0002652) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) + +#### Added +- [endothelial cell of high endothelial venule](http://purl.obolibrary.org/obo/CL_0002652) EquivalentTo [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410037](http://purl.obolibrary.org/obo/UBERON_8410037)) + + +### endothelial cell of lymphatic vessel `http://purl.obolibrary.org/obo/CL_0002138` +#### Removed +- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) EquivalentTo [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001473](http://purl.obolibrary.org/obo/UBERON_0001473)) and ([RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022)) + +#### Added +- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001473](http://purl.obolibrary.org/obo/UBERON_0001473)) + + +### endothelial cell of placenta `http://purl.obolibrary.org/obo/CL_0009092` +#### Removed +- [endothelial cell of placenta](http://purl.obolibrary.org/obo/CL_0009092) SubClassOf [placental epithelial cell](http://purl.obolibrary.org/obo/CL_0002577) + +#### Added +- [endothelial cell of placenta](http://purl.obolibrary.org/obo/CL_0009092) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001987](http://purl.obolibrary.org/obo/UBERON_0001987) + + +### endothelial cell of respiratory system lymphatic vessel `http://purl.obolibrary.org/obo/CL_0009086` +#### Removed +- [endothelial cell of respiratory system lymphatic vessel](http://purl.obolibrary.org/obo/CL_0009086) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +#### Added +- [endothelial cell of respiratory system lymphatic vessel](http://purl.obolibrary.org/obo/CL_0009086) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + +### endothelial cell of sinusoid `http://purl.obolibrary.org/obo/CL_0002262` +#### Removed +- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +#### Added +- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) SubClassOf [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) + + +### endothelial cell of venule `http://purl.obolibrary.org/obo/CL_1000414` +#### Removed +- [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) SubClassOf [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) SubClassOf [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) + + +### endothelial cell of venule of lymph node `http://purl.obolibrary.org/obo/CL_4033000` +#### Removed +- [endothelial cell of venule of lymph node](http://purl.obolibrary.org/obo/CL_4033000) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +#### Added +- [endothelial cell of venule of lymph node](http://purl.obolibrary.org/obo/CL_4033000) SubClassOf [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) + + +### endothelial tip cell `http://purl.obolibrary.org/obo/CL_0000704` +#### Removed +- [endothelial tip cell](http://purl.obolibrary.org/obo/CL_0000704) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009303"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [endothelial tip cell](http://purl.obolibrary.org/obo/CL_0000704) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009303"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enkephalin secreting cell `http://purl.obolibrary.org/obo/CL_0000506` +#### Removed +- [enkephalin secreting cell](http://purl.obolibrary.org/obo/CL_0000506) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009231"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [enkephalin secreting cell](http://purl.obolibrary.org/obo/CL_0000506) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009231"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enteric neuron `http://purl.obolibrary.org/obo/CL_0007011` +#### Removed +- [enteric neuron](http://purl.obolibrary.org/obo/CL_0007011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005775"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [enteric neuron](http://purl.obolibrary.org/obo/CL_0007011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005775"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enterocyte `http://purl.obolibrary.org/obo/CL_0000584` +#### Removed +- [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009269"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009269"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enterocyte of colon `http://purl.obolibrary.org/obo/CL_1000347` + +#### Added +- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000164` +#### Removed +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009097"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009097"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ependymal cell `http://purl.obolibrary.org/obo/CL_0000065` +#### Removed +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009033"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009033"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ependymoglial cell `http://purl.obolibrary.org/obo/CL_0000683` +#### Removed +- [ependymoglial cell](http://purl.obolibrary.org/obo/CL_0000683) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009294"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ependymoglial cell](http://purl.obolibrary.org/obo/CL_0000683) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009294"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epidermal cell `http://purl.obolibrary.org/obo/CL_0000362` +#### Removed +- [epidermal cell](http://purl.obolibrary.org/obo/CL_0000362) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009183"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epidermal cell](http://purl.obolibrary.org/obo/CL_0000362) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009183"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epidermal cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000463` +#### Removed +- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007325"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007325"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epidermal melanocyte `http://purl.obolibrary.org/obo/CL_2000000` +#### Removed +- [epidermal melanocyte](http://purl.obolibrary.org/obo/CL_2000000) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [epidermal melanocyte](http://purl.obolibrary.org/obo/CL_2000000) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### epidermoblast `http://purl.obolibrary.org/obo/CL_0000464` +#### Removed +- [epidermoblast](http://purl.obolibrary.org/obo/CL_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004994"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epidermoblast](http://purl.obolibrary.org/obo/CL_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004994"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epinephrine secreting cell `http://purl.obolibrary.org/obo/CL_0000454` +#### Removed +- [epinephrine secreting cell](http://purl.obolibrary.org/obo/CL_0000454) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009211"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epinephrine secreting cell](http://purl.obolibrary.org/obo/CL_0000454) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009211"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell `http://purl.obolibrary.org/obo/CL_0000066` +#### Removed +- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000124"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009034"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000124"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009034"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell of alveolus of lung `http://purl.obolibrary.org/obo/CL_0010003` +#### Removed +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + +#### Added +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + + +### epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_0002252` +#### Removed +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009400"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009400"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell of lower respiratory tract `http://purl.obolibrary.org/obo/CL_0002632` +#### Removed +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any respiratory epithelial cell that is part of some lower respiratory tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) EquivalentTo [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001558](http://purl.obolibrary.org/obo/UBERON_0001558)) + +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001558](http://purl.obolibrary.org/obo/UBERON_0001558) + +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of some lower respiratory tract epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004815](http://purl.obolibrary.org/obo/UBERON_0004815)) + +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + +- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004815](http://purl.obolibrary.org/obo/UBERON_0004815) + + +### epithelial cell of lung `http://purl.obolibrary.org/obo/CL_0000082` +#### Removed +- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048)) + +- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + +#### Added +- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) + +- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) SubClassOf [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) + + +### epithelial cell of pancreas `http://purl.obolibrary.org/obo/CL_0000083` +#### Removed +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009045"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) + +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + +#### Added +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009045"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) + + +### epithelial cell of proximal tubule `http://purl.obolibrary.org/obo/CL_0002306` +#### Removed +- [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) SubClassOf [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) + +#### Added +- [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions."^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### epithelial cell of proximal tubule segment 1 `http://purl.obolibrary.org/obo/CL_4030009` +#### Removed +- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) + +#### Added +- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23897681"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004196](http://purl.obolibrary.org/obo/UBERON_0004196)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + +- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004196](http://purl.obolibrary.org/obo/UBERON_0004196) + +- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) SubClassOf [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) + + +### epithelial cell of proximal tubule segment 2 `http://purl.obolibrary.org/obo/CL_4030010` +#### Removed +- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) + +#### Added +- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23897681"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31253652"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004197](http://purl.obolibrary.org/obo/UBERON_0004197)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + +- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004197](http://purl.obolibrary.org/obo/UBERON_0004197) + +- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) SubClassOf [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) + + +### epithelial cell of proximal tubule segment 3 `http://purl.obolibrary.org/obo/CL_4030011` +#### Removed +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) + +#### Added +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium, which extends from the medullary rays of the renal cortex into the outer medulla."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001290](http://purl.obolibrary.org/obo/UBERON_0001290)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) SubClassOf [kidney proximal straight tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000839) + +- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) SubClassOf [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) + + +### epithelial cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002202` +#### Removed +- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196)) + +- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196) + +#### Added +- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) + +- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397) + + +### epithelial cell of upper respiratory tract `http://purl.obolibrary.org/obo/CL_0002631` +#### Removed +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any respiratory epithelial cell that is part of some upper respiratory tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) EquivalentTo [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001557](http://purl.obolibrary.org/obo/UBERON_0001557)) + +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001557](http://purl.obolibrary.org/obo/UBERON_0001557) + +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of some upper respiratory tract epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004814](http://purl.obolibrary.org/obo/UBERON_0004814)) + +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004814](http://purl.obolibrary.org/obo/UBERON_0004814) + +- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + + +### erythroblast `http://purl.obolibrary.org/obo/CL_0000765` +#### Removed +- [erythroblast](http://purl.obolibrary.org/obo/CL_0000765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005237"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [erythroblast](http://purl.obolibrary.org/obo/CL_0000765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005237"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### erythroid lineage cell `http://purl.obolibrary.org/obo/CL_0000764` +#### Removed +- [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009325"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009325"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0000038` +#### Removed +- [erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009015"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009015"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### erythrophore `http://purl.obolibrary.org/obo/CL_0000574` +#### Removed +- [erythrophore](http://purl.obolibrary.org/obo/CL_0000574) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009263"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [erythrophore](http://purl.obolibrary.org/obo/CL_0000574) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009263"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### estradiol secreting cell `http://purl.obolibrary.org/obo/CL_0000180` +#### Removed +- [estradiol secreting cell](http://purl.obolibrary.org/obo/CL_0000180) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009110"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [estradiol secreting cell](http://purl.obolibrary.org/obo/CL_0000180) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009110"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### eurydendroid cell `http://purl.obolibrary.org/obo/CL_0000253` +#### Removed +- [eurydendroid cell](http://purl.obolibrary.org/obo/CL_0000253) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009153"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [eurydendroid cell](http://purl.obolibrary.org/obo/CL_0000253) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009153"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### exhausted T cell `http://purl.obolibrary.org/obo/CL_0011025` +#### Removed +- [exhausted T cell](http://purl.obolibrary.org/obo/CL_0011025) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26544946"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [exhausted T cell](http://purl.obolibrary.org/obo/CL_0011025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26544946"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### exocrine cell `http://purl.obolibrary.org/obo/CL_0000152` +#### Removed +- [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009092"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009092"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### extracellular matrix secreting cell `http://purl.obolibrary.org/obo/CL_0000327` +#### Removed +- [extracellular matrix secreting cell](http://purl.obolibrary.org/obo/CL_0000327) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009162"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [extracellular matrix secreting cell](http://purl.obolibrary.org/obo/CL_0000327) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009162"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### extraembryonic cell `http://purl.obolibrary.org/obo/CL_0000349` +#### Removed +- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009176"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009176"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### extramedullary cell `http://purl.obolibrary.org/obo/CL_0000251` +#### Removed +- [extramedullary cell](http://purl.obolibrary.org/obo/CL_0000251) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009152"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [extramedullary cell](http://purl.obolibrary.org/obo/CL_0000251) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009152"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000287` +#### Removed +- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009154"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009154"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### eye_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#eye_upper_slim` + +#### Added +- [eye_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#eye_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes related to specific cell types in the eye."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [eye_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#eye_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### fast muscle cell `http://purl.obolibrary.org/obo/CL_0000190` +#### Removed +- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009117"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009117"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fast muscle myoblast `http://purl.obolibrary.org/obo/CL_0000858` +#### Removed +- [fast muscle myoblast](http://purl.obolibrary.org/obo/CL_0000858) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009369"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fast muscle myoblast](http://purl.obolibrary.org/obo/CL_0000858) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009369"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### female germ line stem cell `http://purl.obolibrary.org/obo/CL_0000022` +#### Removed +- [female germ line stem cell](http://purl.obolibrary.org/obo/CL_0000022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004873"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [female germ line stem cell](http://purl.obolibrary.org/obo/CL_0000022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004873"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### femural osteoblast `http://purl.obolibrary.org/obo/CL_2000057` +#### Removed +- [femural osteoblast](http://purl.obolibrary.org/obo/CL_2000057) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [femural osteoblast](http://purl.obolibrary.org/obo/CL_2000057) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### fenestrated cell `http://purl.obolibrary.org/obo/CL_0000666` +#### Removed +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) [label](http://www.w3.org/2000/01/rdf-schema#label) "fenestrated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009286"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) + +#### Added +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_133"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) [label](http://www.w3.org/2000/01/rdf-schema#label) "fenestrated endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009286"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002064](http://purl.obolibrary.org/obo/PATO_0002064)) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002064](http://purl.obolibrary.org/obo/PATO_0002064) + +- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + + +### fetal pre-type II pneumocyte `http://purl.obolibrary.org/obo/CL_4040003` +#### Removed +- [fetal pre-type II pneumocyte](http://purl.obolibrary.org/obo/CL_4040003) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal pre-type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fetal pre-type II pneumocyte](http://purl.obolibrary.org/obo/CL_4040003) [note](http://purl.obolibrary.org/obo/cl/cl-base#note) "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)."^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fetal pre-type II pneumocyte](http://purl.obolibrary.org/obo/CL_4040003) [note](http://www.geneontology.org/formats/oboInOwl#note) "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fetal pre-type II pneumocyte](http://purl.obolibrary.org/obo/CL_4040003) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal pre-type II pulmonary alveolar epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fetal pre-type II pneumocyte](http://purl.obolibrary.org/obo/CL_4040003) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal pre-type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fibroblast `http://purl.obolibrary.org/obo/CL_0000057` +#### Removed +- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009026"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009026"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### fibroblast of arm `http://purl.obolibrary.org/obo/CL_2000015` +#### Removed +- [fibroblast of arm](http://purl.obolibrary.org/obo/CL_2000015) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [fibroblast of arm](http://purl.obolibrary.org/obo/CL_2000015) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### fibroblast of pedal digit skin `http://purl.obolibrary.org/obo/CL_2000012` +#### Removed +- [fibroblast of pedal digit skin](http://purl.obolibrary.org/obo/CL_2000012) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [fibroblast of pedal digit skin](http://purl.obolibrary.org/obo/CL_2000012) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### fibroblast of peridontal ligament `http://purl.obolibrary.org/obo/CL_2000017` +#### Removed +- [fibroblast of peridontal ligament](http://purl.obolibrary.org/obo/CL_2000017) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [fibroblast of peridontal ligament](http://purl.obolibrary.org/obo/CL_2000017) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### fibroblast of skin of abdomen `http://purl.obolibrary.org/obo/CL_2000013` +#### Removed +- [fibroblast of skin of abdomen](http://purl.obolibrary.org/obo/CL_2000013) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [fibroblast of skin of abdomen](http://purl.obolibrary.org/obo/CL_2000013) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### fibroblast of the reticular layer of dermis `http://purl.obolibrary.org/obo/CL_2000096` +#### Removed +- [fibroblast of the reticular layer of dermis](http://purl.obolibrary.org/obo/CL_2000096) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [fibroblast of the reticular layer of dermis](http://purl.obolibrary.org/obo/CL_2000096) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### fibroblast of upper leg skin `http://purl.obolibrary.org/obo/CL_2000014` +#### Removed +- [fibroblast of upper leg skin](http://purl.obolibrary.org/obo/CL_2000014) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [fibroblast of upper leg skin](http://purl.obolibrary.org/obo/CL_2000014) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### follicle cell of egg chamber `http://purl.obolibrary.org/obo/CL_0000477` +#### Removed +- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004904"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004904"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### follicle stem cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000441` +#### Removed +- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004903"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004903"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### folliculostellate cell `http://purl.obolibrary.org/obo/CL_0000642` +#### Removed +- [folliculostellate cell](http://purl.obolibrary.org/obo/CL_0000642) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009281"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [folliculostellate cell](http://purl.obolibrary.org/obo/CL_0000642) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009281"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### foreskin melanocyte `http://purl.obolibrary.org/obo/CL_2000045` +#### Removed +- [foreskin melanocyte](http://purl.obolibrary.org/obo/CL_2000045) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [foreskin melanocyte](http://purl.obolibrary.org/obo/CL_2000045) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### gallbladder fibroblast `http://purl.obolibrary.org/obo/CL_2000069` +#### Removed +- [gallbladder fibroblast](http://purl.obolibrary.org/obo/CL_2000069) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [gallbladder fibroblast](http://purl.obolibrary.org/obo/CL_2000069) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### gamete `http://purl.obolibrary.org/obo/CL_0000300` +#### Removed +- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009156"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005412"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005412"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009156"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000798` +#### Removed +- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009336"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009336"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gamma-delta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0000801` +#### Removed +- [gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000801) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009339"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000801) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009339"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ganglion mother cell `http://purl.obolibrary.org/obo/CL_0000469` +#### Removed +- [ganglion mother cell](http://purl.obolibrary.org/obo/CL_0000469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005149"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ganglion mother cell](http://purl.obolibrary.org/obo/CL_0000469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005149"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### garland cell `http://purl.obolibrary.org/obo/CL_0000486` +#### Removed +- [garland cell](http://purl.obolibrary.org/obo/CL_0000486) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005059"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [garland cell](http://purl.obolibrary.org/obo/CL_0000486) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005059"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gastrula cell `http://purl.obolibrary.org/obo/CL_0000361` +#### Removed +- [gastrula cell](http://purl.obolibrary.org/obo/CL_0000361) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009182"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gastrula cell](http://purl.obolibrary.org/obo/CL_0000361) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009182"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### general_cell_types_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#general_cell_types_upper_slim` + +#### Added +- [general_cell_types_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#general_cell_types_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes of cell types in the cell ontology."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [general_cell_types_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#general_cell_types_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### germ line cell `http://purl.obolibrary.org/obo/CL_0000039` +#### Removed +- [germ line cell](http://purl.obolibrary.org/obo/CL_0000039) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009016"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [germ line cell](http://purl.obolibrary.org/obo/CL_0000039) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009016"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### germ line stem cell `http://purl.obolibrary.org/obo/CL_0000014` +#### Removed +- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004861"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005956"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005956"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004861"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ghrelin secreting cell `http://purl.obolibrary.org/obo/CL_0005018` +#### Removed +- [ghrelin secreting cell](http://purl.obolibrary.org/obo/CL_0005018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005599"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ghrelin secreting cell](http://purl.obolibrary.org/obo/CL_0005018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005599"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glial cell `http://purl.obolibrary.org/obo/CL_0000125` +#### Removed +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005144"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009073"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005144"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009073"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glioblast `http://purl.obolibrary.org/obo/CL_0000030` +#### Removed +- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009010"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009010"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glioblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000340` +#### Removed +- [glioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000340) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005145"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000340) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005145"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glioblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000339` +#### Removed +- [glioblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000339) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009169"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glioblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000339) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009169"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glomerular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001005` +#### Removed +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [kidney glomerular epithelial cell](http://purl.obolibrary.org/obo/CL_1000510) + +#### Added +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) + + +### glomerular cell `http://purl.obolibrary.org/obo/CL_1000746` +#### Removed +- [glomerular cell](http://purl.obolibrary.org/obo/CL_1000746) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glomerular cell](http://purl.obolibrary.org/obo/CL_1000746) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) + + +### glomerular endothelial cell `http://purl.obolibrary.org/obo/CL_0002188` +#### Removed +- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [glomerular cell](http://purl.obolibrary.org/obo/CL_1000746) + +#### Added +- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + +- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000074](http://purl.obolibrary.org/obo/UBERON_0000074) + + +### glucagon secreting cell `http://purl.obolibrary.org/obo/CL_0000170` +#### Removed +- [glucagon secreting cell](http://purl.obolibrary.org/obo/CL_0000170) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009103"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glucagon secreting cell](http://purl.obolibrary.org/obo/CL_0000170) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009103"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glucocorticoid secreting cell `http://purl.obolibrary.org/obo/CL_0000460` +#### Removed +- [glucocorticoid secreting cell](http://purl.obolibrary.org/obo/CL_0000460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009215"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glucocorticoid secreting cell](http://purl.obolibrary.org/obo/CL_0000460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009215"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glutamatergic neuron `http://purl.obolibrary.org/obo/CL_0000679` +#### Removed +- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100291"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009290"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100291"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009290"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glycinergic neuron `http://purl.obolibrary.org/obo/CL_1001509` +#### Removed +- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00048032"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009396"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009396"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00048032"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glycosaminoglycan secreting cell `http://purl.obolibrary.org/obo/CL_0000153` +#### Removed +- [glycosaminoglycan secreting cell](http://purl.obolibrary.org/obo/CL_0000153) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009093"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [glycosaminoglycan secreting cell](http://purl.obolibrary.org/obo/CL_0000153) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009093"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### goblet cell `http://purl.obolibrary.org/obo/CL_0000160` +#### Removed +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009094"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009094"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gonadtroph `http://purl.obolibrary.org/obo/CL_0000437` +#### Removed +- [gonadtroph](http://purl.obolibrary.org/obo/CL_0000437) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009202"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gonadtroph](http://purl.obolibrary.org/obo/CL_0000437) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009202"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### granule cell `http://purl.obolibrary.org/obo/CL_0000120` +#### Removed +- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009070"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009070"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### granulocyte `http://purl.obolibrary.org/obo/CL_0000094` +#### Removed +- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009048"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009048"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### granulocyte monocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000557` +#### Removed +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009251"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009251"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### granulosa cell `http://purl.obolibrary.org/obo/CL_0000501` +#### Removed +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009227"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009227"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) + + +### green sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000496` +#### Removed +- [green sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000496) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009223"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [green sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000496) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009223"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gut absorptive cell `http://purl.obolibrary.org/obo/CL_0000677` +#### Removed +- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009289"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009289"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### gut endothelial cell `http://purl.obolibrary.org/obo/CL_0000131` +#### Removed +- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009078"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009078"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hair follicle dermal papilla cell of scalp `http://purl.obolibrary.org/obo/CL_2000083` +#### Removed +- [hair follicle dermal papilla cell of scalp](http://purl.obolibrary.org/obo/CL_2000083) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [hair follicle dermal papilla cell of scalp](http://purl.obolibrary.org/obo/CL_2000083) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### hair follicular keratinocyte `http://purl.obolibrary.org/obo/CL_2000092` +#### Removed +- [hair follicular keratinocyte](http://purl.obolibrary.org/obo/CL_2000092) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [hair follicular keratinocyte](http://purl.obolibrary.org/obo/CL_2000092) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### hatching gland cell `http://purl.obolibrary.org/obo/CL_0000249` +#### Removed +- [hatching gland cell](http://purl.obolibrary.org/obo/CL_0000249) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009151"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hatching gland cell](http://purl.obolibrary.org/obo/CL_0000249) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009151"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hematopoietic cell `http://purl.obolibrary.org/obo/CL_0000988` +#### Removed +- [hematopoietic cell](http://purl.obolibrary.org/obo/CL_0000988) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005830"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hematopoietic cell](http://purl.obolibrary.org/obo/CL_0000988) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005830"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hematopoietic multipotent progenitor cell `http://purl.obolibrary.org/obo/CL_0000837` +#### Removed +- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009354"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009354"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0000037` +#### Removed +- [hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0000037) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009014"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0000037) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009014"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hemocyte (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000387` +#### Removed +- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005063"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005063"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hepatic stellate cell `http://purl.obolibrary.org/obo/CL_0000632` +#### Removed +- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009279"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009279"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hepatocyte `http://purl.obolibrary.org/obo/CL_0000182` +#### Removed +- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009111"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009111"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hindlimb stylopod vein endothelial cell `http://purl.obolibrary.org/obo/CL_2000076` +#### Removed +- [hindlimb stylopod vein endothelial cell](http://purl.obolibrary.org/obo/CL_2000076) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [hindlimb stylopod vein endothelial cell](http://purl.obolibrary.org/obo/CL_2000076) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### histaminergic neuron `http://purl.obolibrary.org/obo/CL_0011110` +#### Removed +- [histaminergic neuron](http://purl.obolibrary.org/obo/CL_0011110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007367"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [histaminergic neuron](http://purl.obolibrary.org/obo/CL_0011110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007367"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### histoblast `http://purl.obolibrary.org/obo/CL_0000373` +#### Removed +- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001789"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001789"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hypertrophic chondrocyte `http://purl.obolibrary.org/obo/CL_0000743` +#### Removed +- [hypertrophic chondrocyte](http://purl.obolibrary.org/obo/CL_0000743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009313"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hypertrophic chondrocyte](http://purl.obolibrary.org/obo/CL_0000743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009313"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hypocretin-secreting neuron `http://purl.obolibrary.org/obo/CL_0011109` +#### Removed +- [hypocretin-secreting neuron](http://purl.obolibrary.org/obo/CL_0011109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005778"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [hypocretin-secreting neuron](http://purl.obolibrary.org/obo/CL_0011109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005778"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### hypothalamus cell `http://purl.obolibrary.org/obo/CL_2000030` +#### Removed +- [hypothalamus cell](http://purl.obolibrary.org/obo/CL_2000030) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [hypothalamus cell](http://purl.obolibrary.org/obo/CL_2000030) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### imaginal disc cell `http://purl.obolibrary.org/obo/CL_0000429` +#### Removed +- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007108"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007108"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature B cell `http://purl.obolibrary.org/obo/CL_0000816` +#### Removed +- [immature B cell](http://purl.obolibrary.org/obo/CL_0000816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009343"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature B cell](http://purl.obolibrary.org/obo/CL_0000816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009343"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature Schwann cell `http://purl.obolibrary.org/obo/CL_0002377` +#### Removed +- [immature Schwann cell](http://purl.obolibrary.org/obo/CL_0002377) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001725"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature Schwann cell](http://purl.obolibrary.org/obo/CL_0002377) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001725"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000799` +#### Removed +- [immature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000799) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009337"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000799) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009337"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature natural killer cell `http://purl.obolibrary.org/obo/CL_0000823` +#### Removed +- [immature natural killer cell](http://purl.obolibrary.org/obo/CL_0000823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009346"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature natural killer cell](http://purl.obolibrary.org/obo/CL_0000823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009346"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### immature neutrophil `http://purl.obolibrary.org/obo/CL_0000776` +#### Removed +- [immature neutrophil](http://purl.obolibrary.org/obo/CL_0000776) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009328"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [immature neutrophil](http://purl.obolibrary.org/obo/CL_0000776) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009328"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### inhibitory interneuron `http://purl.obolibrary.org/obo/CL_0000498` +#### Removed +- [inhibitory interneuron](http://purl.obolibrary.org/obo/CL_0000498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009225"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [inhibitory interneuron](http://purl.obolibrary.org/obo/CL_0000498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009225"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### inner cell mass cell `http://purl.obolibrary.org/obo/CL_2000020` +#### Removed +- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### insect flight muscle cell `http://purl.obolibrary.org/obo/CL_0000196` +#### Removed +- [insect flight muscle cell](http://purl.obolibrary.org/obo/CL_0000196) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003360"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [insect flight muscle cell](http://purl.obolibrary.org/obo/CL_0000196) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003360"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### insulating cell `http://purl.obolibrary.org/obo/CL_0000217` +#### Removed +- [insulating cell](http://purl.obolibrary.org/obo/CL_0000217) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009134"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [insulating cell](http://purl.obolibrary.org/obo/CL_0000217) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009134"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### insulin secreting cell `http://purl.obolibrary.org/obo/CL_0000168` +#### Removed +- [insulin secreting cell](http://purl.obolibrary.org/obo/CL_0000168) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009101"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [insulin secreting cell](http://purl.obolibrary.org/obo/CL_0000168) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009101"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### interfollicle cell `http://purl.obolibrary.org/obo/CL_0000674` +#### Removed +- [interfollicle cell](http://purl.obolibrary.org/obo/CL_0000674) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004910"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [interfollicle cell](http://purl.obolibrary.org/obo/CL_0000674) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004910"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### interneuromast cell `http://purl.obolibrary.org/obo/CL_0000854` +#### Removed +- [interneuromast cell](http://purl.obolibrary.org/obo/CL_0000854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009365"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [interneuromast cell](http://purl.obolibrary.org/obo/CL_0000854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009365"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### interneuron `http://purl.obolibrary.org/obo/CL_0000099` +#### Removed +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005125"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009051"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009051"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005125"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### intestinal epithelial cell `http://purl.obolibrary.org/obo/CL_0002563` +#### Removed +- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009399"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009399"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### intrahepatic cholangiocyte `http://purl.obolibrary.org/obo/CL_0002538` +#### Removed +- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009379"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009379"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### invertebrate nurse cell `http://purl.obolibrary.org/obo/CL_0000026` +#### Removed +- [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004878"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004878"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ionocyte `http://purl.obolibrary.org/obo/CL_0005006` +#### Removed +- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005323"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005323"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### iridoblast `http://purl.obolibrary.org/obo/CL_0005001` +#### Removed +- [iridoblast](http://purl.obolibrary.org/obo/CL_0005001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005328"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [iridoblast](http://purl.obolibrary.org/obo/CL_0005001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005328"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### iridophore `http://purl.obolibrary.org/obo/CL_0000431` +#### Removed +- [iridophore](http://purl.obolibrary.org/obo/CL_0000431) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009199"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [iridophore](http://purl.obolibrary.org/obo/CL_0000431) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009199"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### juvenile hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000482` +#### Removed +- [juvenile hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000482) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00058020"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [juvenile hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000482) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00058020"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### keratin accumulating cell `http://purl.obolibrary.org/obo/CL_0000311` +#### Removed +- [keratin accumulating cell](http://purl.obolibrary.org/obo/CL_0000311) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009157"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [keratin accumulating cell](http://purl.obolibrary.org/obo/CL_0000311) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009157"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### keratinocyte `http://purl.obolibrary.org/obo/CL_0000312` +#### Removed +- [keratinocyte](http://purl.obolibrary.org/obo/CL_0000312) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009158"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [keratinocyte](http://purl.obolibrary.org/obo/CL_0000312) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009158"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006` +#### Removed +- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) + +#### Added +- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + + +### kidney arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001066` +#### Removed +- [kidney arteriole smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001066) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) + + + +### kidney artery smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001064` +#### Removed +- [kidney artery smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001064) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) + + + +### kidney blood vessel cell `http://purl.obolibrary.org/obo/CL_1000854` +#### Removed +- [kidney blood vessel cell](http://purl.obolibrary.org/obo/CL_1000854) SubClassOf [renal cortical epithelial cell](http://purl.obolibrary.org/obo/CL_0002584) + + + +### kidney cell `http://purl.obolibrary.org/obo/CL_1000497` +#### Removed +- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009389"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009389"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney corpuscule cell `http://purl.obolibrary.org/obo/CL_1000612` +#### Removed +- [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) SubClassOf [renal cortical epithelial cell](http://purl.obolibrary.org/obo/CL_0002584) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) SubClassOf [renal cortical epithelial cell](http://purl.obolibrary.org/obo/CL_0002584) + + +### kidney cortex artery cell `http://purl.obolibrary.org/obo/CL_1001045` +#### Removed +- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + +- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) + + +### kidney cortex peritubular capillary cell `http://purl.obolibrary.org/obo/CL_1001124` +#### Removed +- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) SubClassOf [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + +- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) SubClassOf [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) + + +### kidney cortex vein cell `http://purl.obolibrary.org/obo/CL_1001052` + +#### Added +- [kidney cortex vein cell](http://purl.obolibrary.org/obo/CL_1001052) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + + +### kidney efferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001009` +#### Removed +- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) + +- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + +- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) + + +### kidney efferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001099` +#### Removed +- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) SubClassOf [endothelial cell of arteriole](http://purl.obolibrary.org/obo/CL_1000412) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) SubClassOf [endothelial cell of arteriole](http://purl.obolibrary.org/obo/CL_1000412) + + +### kidney epithelial cell `http://purl.obolibrary.org/obo/CL_0002518` +#### Removed +- [kidney epithelial cell](http://purl.obolibrary.org/obo/CL_0002518) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009374"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney epithelial cell](http://purl.obolibrary.org/obo/CL_0002518) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009374"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney granular cell `http://purl.obolibrary.org/obo/CL_0000648` +#### Removed +- [kidney granular cell](http://purl.obolibrary.org/obo/CL_0000648) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005238"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney granular cell](http://purl.obolibrary.org/obo/CL_0000648) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005238"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney interstitial cell `http://purl.obolibrary.org/obo/CL_1000500` +#### Removed +- [kidney interstitial cell](http://purl.obolibrary.org/obo/CL_1000500) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009390"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney interstitial cell](http://purl.obolibrary.org/obo/CL_1000500) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009390"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney medulla cell `http://purl.obolibrary.org/obo/CL_1000504` +#### Removed +- [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009391"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009391"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### kidney proximal convoluted tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000838` +#### Removed +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) EquivalentTo [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001287](http://purl.obolibrary.org/obo/UBERON_0001287)) + +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) EquivalentTo [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001287](http://purl.obolibrary.org/obo/UBERON_0001287)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + +- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) SubClassOf [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) + + +### kidney venous system smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001068` +#### Removed +- [kidney venous system smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001068) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) + + + +### kidney_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#kidney_upper_slim` + +#### Added +- [kidney_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#kidney_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes related to specific cell types in the kidney"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [kidney_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#kidney_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### lamellocyte `http://purl.obolibrary.org/obo/CL_0000396` +#### Removed +- [lamellocyte](http://purl.obolibrary.org/obo/CL_0000396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001687"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lamellocyte](http://purl.obolibrary.org/obo/CL_0000396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001687"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### lamp5 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023011` +#### Removed +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + +#### Added +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) + + +### lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_2000031` +#### Removed +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### lens fiber cell `http://purl.obolibrary.org/obo/CL_0011004` +#### Removed +- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009401"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009401"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### leptomeningeal cell `http://purl.obolibrary.org/obo/CL_0000708` +#### Removed +- [leptomeningeal cell](http://purl.obolibrary.org/obo/CL_0000708) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009305"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [leptomeningeal cell](http://purl.obolibrary.org/obo/CL_0000708) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009305"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### leucoblast `http://purl.obolibrary.org/obo/CL_0005003` +#### Removed +- [leucoblast](http://purl.obolibrary.org/obo/CL_0005003) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005329"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [leucoblast](http://purl.obolibrary.org/obo/CL_0005003) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005329"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### leucophore `http://purl.obolibrary.org/obo/CL_0000571` +#### Removed +- [leucophore](http://purl.obolibrary.org/obo/CL_0000571) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009261"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [leucophore](http://purl.obolibrary.org/obo/CL_0000571) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009261"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### leukocyte `http://purl.obolibrary.org/obo/CL_0000738` +#### Removed +- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009309"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009309"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ligament cell `http://purl.obolibrary.org/obo/CL_0000384` +#### Removed +- [ligament cell](http://purl.obolibrary.org/obo/CL_0000384) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009188"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [ligament cell](http://purl.obolibrary.org/obo/CL_0000384) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009188"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### limb basal cell of epidermis `http://purl.obolibrary.org/obo/CL_2000033` +#### Removed +- [limb basal cell of epidermis](http://purl.obolibrary.org/obo/CL_2000033) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [limb basal cell of epidermis](http://purl.obolibrary.org/obo/CL_2000033) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### lining cell `http://purl.obolibrary.org/obo/CL_0000213` +#### Removed +- [lining cell](http://purl.obolibrary.org/obo/CL_0000213) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009130"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lining cell](http://purl.obolibrary.org/obo/CL_0000213) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009130"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### liver dendritic cell `http://purl.obolibrary.org/obo/CL_2000055` +#### Removed +- [liver dendritic cell](http://purl.obolibrary.org/obo/CL_2000055) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [liver dendritic cell](http://purl.obolibrary.org/obo/CL_2000055) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### lung endothelial cell `http://purl.obolibrary.org/obo/CL_1001567` +#### Removed +- [lung endothelial cell](http://purl.obolibrary.org/obo/CL_1001567) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + + +### lung goblet cell `http://purl.obolibrary.org/obo/CL_1000143` +#### Removed +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any goblet cell that is part of some lung."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048)) + +#### Added +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any goblet cell that is part of some lung epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) + + +### lung microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000016` +#### Removed +- [lung microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000016) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [lung microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000016) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### lung neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000223` +#### Removed +- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + + +### luteinizing hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000438` +#### Removed +- [luteinizing hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000438) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009203"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [luteinizing hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000438) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009203"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### lymph gland hemocyte `http://purl.obolibrary.org/obo/CL_0000735` +#### Removed +- [lymph gland hemocyte](http://purl.obolibrary.org/obo/CL_0000735) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005917"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lymph gland hemocyte](http://purl.obolibrary.org/obo/CL_0000735) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005917"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### lymph node lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0009115` +#### Removed +- [lymph node lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0009115) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + +- [lymph node lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0009115) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001473](http://purl.obolibrary.org/obo/UBERON_0001473) + +#### Added +- [lymph node lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0009115) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + +### lymphangioblast `http://purl.obolibrary.org/obo/CL_0005020` +#### Removed +- [lymphangioblast](http://purl.obolibrary.org/obo/CL_0005020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009393"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lymphangioblast](http://purl.obolibrary.org/obo/CL_0005020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009393"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### lymphatic endothelial cell of medulla ceiling `http://purl.obolibrary.org/obo/CL_0009110` +#### Removed +- [lymphatic endothelial cell of medulla ceiling](http://purl.obolibrary.org/obo/CL_0009110) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + + +### lymphatic endothelial cell of subcapsular sinus ceiling `http://purl.obolibrary.org/obo/CL_0009107` +#### Removed +- [lymphatic endothelial cell of subcapsular sinus ceiling](http://purl.obolibrary.org/obo/CL_0009107) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + + +### lymphatic endothelial cell of subcapsular sinus floor `http://purl.obolibrary.org/obo/CL_0009108` +#### Removed +- [lymphatic endothelial cell of subcapsular sinus floor](http://purl.obolibrary.org/obo/CL_0009108) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + + +### lymphatic endothelial cell of trabecula `http://purl.obolibrary.org/obo/CL_0009109` +#### Removed +- [lymphatic endothelial cell of trabecula](http://purl.obolibrary.org/obo/CL_0009109) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) + + + +### lymphocyte `http://purl.obolibrary.org/obo/CL_0000542` +#### Removed +- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009250"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009250"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### lymphoid lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0000838` +#### Removed +- [lymphoid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000838) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009355"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [lymphoid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000838) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009355"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### macroglial cell `http://purl.obolibrary.org/obo/CL_0000126` +#### Removed +- [macroglial cell](http://purl.obolibrary.org/obo/CL_0000126) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009074"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [macroglial cell](http://purl.obolibrary.org/obo/CL_0000126) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009074"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### macrophage `http://purl.obolibrary.org/obo/CL_0000235` +#### Removed +- [macrophage](http://purl.obolibrary.org/obo/CL_0000235) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009141"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [macrophage](http://purl.obolibrary.org/obo/CL_0000235) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009141"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### male germ line stem cell `http://purl.obolibrary.org/obo/CL_0000016` +#### Removed +- [male germ line stem cell](http://purl.obolibrary.org/obo/CL_0000016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004929"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [male germ line stem cell](http://purl.obolibrary.org/obo/CL_0000016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004929"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mammary microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000071` +#### Removed +- [mammary microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000071) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [mammary microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000071) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### mapping_justification `https://w3id.org/sssom/mapping_justification` + +#### Added +- AnnotationProperty: [mapping_justification](https://w3id.org/sssom/mapping_justification) + + +### mapping_justification `http://purl.obolibrary.org/obo/mapping_justification` +#### Removed +- AnnotationProperty: [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) + + + +### mature B cell `http://purl.obolibrary.org/obo/CL_0000785` +#### Removed +- [mature B cell](http://purl.obolibrary.org/obo/CL_0000785) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009331"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature B cell](http://purl.obolibrary.org/obo/CL_0000785) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009331"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000800` +#### Removed +- [mature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000800) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009338"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000800) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009338"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature natural killer cell `http://purl.obolibrary.org/obo/CL_0000824` +#### Removed +- [mature natural killer cell](http://purl.obolibrary.org/obo/CL_0000824) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009347"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature natural killer cell](http://purl.obolibrary.org/obo/CL_0000824) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009347"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mature neutrophil `http://purl.obolibrary.org/obo/CL_0000096` +#### Removed +- [mature neutrophil](http://purl.obolibrary.org/obo/CL_0000096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009049"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mature neutrophil](http://purl.obolibrary.org/obo/CL_0000096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009049"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mechanoreceptor cell `http://purl.obolibrary.org/obo/CL_0000199` +#### Removed +- [mechanoreceptor cell](http://purl.obolibrary.org/obo/CL_0000199) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009120"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mechanoreceptor cell](http://purl.obolibrary.org/obo/CL_0000199) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009120"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### megakaryocyte-erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0000050` +#### Removed +- [megakaryocyte-erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009022"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [megakaryocyte-erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009022"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### melanoblast `http://purl.obolibrary.org/obo/CL_0000541` +#### Removed +- [melanoblast](http://purl.obolibrary.org/obo/CL_0000541) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009249"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [melanoblast](http://purl.obolibrary.org/obo/CL_0000541) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009249"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### melanocyte `http://purl.obolibrary.org/obo/CL_0000148` +#### Removed +- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009091"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009091"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### melanocyte of skin of face `http://purl.obolibrary.org/obo/CL_2000081` +#### Removed +- [melanocyte of skin of face](http://purl.obolibrary.org/obo/CL_2000081) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [melanocyte of skin of face](http://purl.obolibrary.org/obo/CL_2000081) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### melanocyte stimulating hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000440` +#### Removed +- [melanocyte stimulating hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000440) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009205"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [melanocyte stimulating hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000440) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009205"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### memory B cell `http://purl.obolibrary.org/obo/CL_0000787` +#### Removed +- [memory B cell](http://purl.obolibrary.org/obo/CL_0000787) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009333"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [memory B cell](http://purl.obolibrary.org/obo/CL_0000787) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009333"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### memory T cell `http://purl.obolibrary.org/obo/CL_0000813` +#### Removed +- [memory T cell](http://purl.obolibrary.org/obo/CL_0000813) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009342"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [memory T cell](http://purl.obolibrary.org/obo/CL_0000813) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009342"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesangial cell `http://purl.obolibrary.org/obo/CL_0000650` +#### Removed +- [mesangial cell](http://purl.obolibrary.org/obo/CL_0000650) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009283"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesangial cell](http://purl.obolibrary.org/obo/CL_0000650) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009283"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesenchymal lymphangioblast `http://purl.obolibrary.org/obo/CL_0005021` +#### Removed +- [mesenchymal lymphangioblast](http://purl.obolibrary.org/obo/CL_0005021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009394"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesenchymal lymphangioblast](http://purl.obolibrary.org/obo/CL_0005021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009394"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesenchymal stem cell `http://purl.obolibrary.org/obo/CL_0000134` +#### Removed +- [mesenchymal stem cell](http://purl.obolibrary.org/obo/CL_0000134) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009081"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesenchymal stem cell](http://purl.obolibrary.org/obo/CL_0000134) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009081"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesenchymal stem cell of abdominal adipose tissue `http://purl.obolibrary.org/obo/CL_2000080` +#### Removed +- [mesenchymal stem cell of abdominal adipose tissue](http://purl.obolibrary.org/obo/CL_2000080) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [mesenchymal stem cell of abdominal adipose tissue](http://purl.obolibrary.org/obo/CL_2000080) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### mesenchymal stem cell of femoral bone marrow `http://purl.obolibrary.org/obo/CL_2000079` +#### Removed +- [mesenchymal stem cell of femoral bone marrow](http://purl.obolibrary.org/obo/CL_2000079) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [mesenchymal stem cell of femoral bone marrow](http://purl.obolibrary.org/obo/CL_2000079) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### mesenchyme condensation cell `http://purl.obolibrary.org/obo/CL_0000335` +#### Removed +- [mesenchyme condensation cell](http://purl.obolibrary.org/obo/CL_0000335) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009166"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesenchyme condensation cell](http://purl.obolibrary.org/obo/CL_0000335) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009166"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### meso-epithelial cell `http://purl.obolibrary.org/obo/CL_0002078` +#### Removed +- [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009388"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009388"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesodermal cell `http://purl.obolibrary.org/obo/CL_0000222` +#### Removed +- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009138"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009138"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesothelial cell `http://purl.obolibrary.org/obo/CL_0000077` +#### Removed +- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009040"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009040"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mesothelial cell of visceral pleura `http://purl.obolibrary.org/obo/CL_1000493` +#### Removed +- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + + +### microglial cell `http://purl.obolibrary.org/obo/CL_0000129` +#### Removed +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009077"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009077"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### micropylar cell `http://purl.obolibrary.org/obo/CL_0007022` +#### Removed +- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005239"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005239"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000008` +#### Removed +- [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### microvillous olfactory receptor neuron `http://purl.obolibrary.org/obo/CL_0000848` +#### Removed +- [microvillous olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000848) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009359"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [microvillous olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000848) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009359"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### midbrain dopaminergic neuron `http://purl.obolibrary.org/obo/CL_2000097` +#### Removed +- [midbrain dopaminergic neuron](http://purl.obolibrary.org/obo/CL_2000097) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [midbrain dopaminergic neuron](http://purl.obolibrary.org/obo/CL_2000097) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### migratory cardiac neural crest cell `http://purl.obolibrary.org/obo/CL_2000073` +#### Removed +- [migratory cardiac neural crest cell](http://purl.obolibrary.org/obo/CL_2000073) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [migratory cardiac neural crest cell](http://purl.obolibrary.org/obo/CL_2000073) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### migratory cranial neural crest cell `http://purl.obolibrary.org/obo/CL_0000008` +#### Removed +- [migratory cranial neural crest cell](http://purl.obolibrary.org/obo/CL_0000008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007091"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [migratory cranial neural crest cell](http://purl.obolibrary.org/obo/CL_0000008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007091"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### migratory neural crest cell `http://purl.obolibrary.org/obo/CL_0000333` +#### Removed +- [migratory neural crest cell](http://purl.obolibrary.org/obo/CL_0000333) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007086"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [migratory neural crest cell](http://purl.obolibrary.org/obo/CL_0000333) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007086"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### migratory trunk neural crest cell `http://purl.obolibrary.org/obo/CL_0000011` +#### Removed +- [migratory trunk neural crest cell](http://purl.obolibrary.org/obo/CL_0000011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007095"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [migratory trunk neural crest cell](http://purl.obolibrary.org/obo/CL_0000011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007095"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### monoblast `http://purl.obolibrary.org/obo/CL_0000040` +#### Removed +- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009017"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009017"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### monocyte `http://purl.obolibrary.org/obo/CL_0000576` +#### Removed +- [monocyte](http://purl.obolibrary.org/obo/CL_0000576) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009265"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [monocyte](http://purl.obolibrary.org/obo/CL_0000576) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009265"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mononuclear cell `http://purl.obolibrary.org/obo/CL_0000842` +#### Removed +- [mononuclear cell](http://purl.obolibrary.org/obo/CL_0000842) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009357"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mononuclear cell](http://purl.obolibrary.org/obo/CL_0000842) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009357"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mononuclear cell of umbilical cord `http://purl.obolibrary.org/obo/CL_2000085` +#### Removed +- [mononuclear cell of umbilical cord](http://purl.obolibrary.org/obo/CL_2000085) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [mononuclear cell of umbilical cord](http://purl.obolibrary.org/obo/CL_2000085) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### mononuclear odontoclast `http://purl.obolibrary.org/obo/CL_0000781` +#### Removed +- [mononuclear odontoclast](http://purl.obolibrary.org/obo/CL_0000781) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009330"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mononuclear odontoclast](http://purl.obolibrary.org/obo/CL_0000781) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009330"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mononuclear osteoclast `http://purl.obolibrary.org/obo/CL_0000778` +#### Removed +- [mononuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000778) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009329"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mononuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000778) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009329"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_0000113` +#### Removed +- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009064"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009064"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### motile cell `http://purl.obolibrary.org/obo/CL_0000219` +#### Removed +- [motile cell](http://purl.obolibrary.org/obo/CL_0000219) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009136"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [motile cell](http://purl.obolibrary.org/obo/CL_0000219) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009136"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### motor neuron `http://purl.obolibrary.org/obo/CL_0000100` +#### Removed +- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009052"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005123"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009052"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005123"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mucus secreting cell `http://purl.obolibrary.org/obo/CL_0000319` +#### Removed +- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009159"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009159"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### multi fate stem cell `http://purl.obolibrary.org/obo/CL_0000048` +#### Removed +- [multi fate stem cell](http://purl.obolibrary.org/obo/CL_0000048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009020"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [multi fate stem cell](http://purl.obolibrary.org/obo/CL_0000048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009020"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012` +#### Removed +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005242"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005242"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### multi-potent skeletal muscle stem cell `http://purl.obolibrary.org/obo/CL_0000355` +#### Removed +- [multi-potent skeletal muscle stem cell](http://purl.obolibrary.org/obo/CL_0000355) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009179"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [multi-potent skeletal muscle stem cell](http://purl.obolibrary.org/obo/CL_0000355) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009179"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### multipolar neuron `http://purl.obolibrary.org/obo/CL_0000104` +#### Removed +- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009056"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009056"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mural cell `http://purl.obolibrary.org/obo/CL_0008034` +#### Removed +- [mural cell](http://purl.obolibrary.org/obo/CL_0008034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005944"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [mural cell](http://purl.obolibrary.org/obo/CL_0008034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005944"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### mural granulosa cell `http://purl.obolibrary.org/obo/CL_4033067` + +#### Added +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [label](http://www.w3.org/2000/01/rdf-schema#label) "mural granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27815559"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033067"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mural GC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EFO:0005289"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [date](http://purl.org/dc/terms/date) "2024-06-07T12:15:13Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MGC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1530/REP-16-0500"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) + +- Class: [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) + +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) + + +### muscle cell `http://purl.obolibrary.org/obo/CL_0000187` +#### Removed +- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005074"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009114"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005074"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009114"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### muscle precursor cell `http://purl.obolibrary.org/obo/CL_0000680` +#### Removed +- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009291"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009291"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myelinating Schwann cell `http://purl.obolibrary.org/obo/CL_0000218` +#### Removed +- [myelinating Schwann cell](http://purl.obolibrary.org/obo/CL_0000218) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009135"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myelinating Schwann cell](http://purl.obolibrary.org/obo/CL_0000218) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009135"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myeloblast `http://purl.obolibrary.org/obo/CL_0000835` +#### Removed +- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009353"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009353"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myeloid cell `http://purl.obolibrary.org/obo/CL_0000763` +#### Removed +- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009324"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009324"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myeloid leukocyte `http://purl.obolibrary.org/obo/CL_0000766` +#### Removed +- [myeloid leukocyte](http://purl.obolibrary.org/obo/CL_0000766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009326"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myeloid leukocyte](http://purl.obolibrary.org/obo/CL_0000766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009326"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myeloid lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0000839` +#### Removed +- [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009356"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009356"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myoblast `http://purl.obolibrary.org/obo/CL_0000056` +#### Removed +- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005083"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009025"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005083"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009025"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myoepithelial cell `http://purl.obolibrary.org/obo/CL_0000185` +#### Removed +- [myoepithelial cell](http://purl.obolibrary.org/obo/CL_0000185) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009113"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myoepithelial cell](http://purl.obolibrary.org/obo/CL_0000185) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009113"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### myotube `http://purl.obolibrary.org/obo/CL_0002372` +#### Removed +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### naive B cell `http://purl.obolibrary.org/obo/CL_0000788` +#### Removed +- [naive B cell](http://purl.obolibrary.org/obo/CL_0000788) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009334"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [naive B cell](http://purl.obolibrary.org/obo/CL_0000788) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009334"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa `http://purl.obolibrary.org/obo/CL_2000094` +#### Removed +- [nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa](http://purl.obolibrary.org/obo/CL_2000094) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa](http://purl.obolibrary.org/obo/CL_2000094) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + +- [nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa](http://purl.obolibrary.org/obo/CL_2000094) SubClassOf [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) + + +### nasal mucosa goblet cell `http://purl.obolibrary.org/obo/CL_0002480` + +#### Added +- [nasal mucosa goblet cell](http://purl.obolibrary.org/obo/CL_0002480) SubClassOf [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) + + +### natural killer cell `http://purl.obolibrary.org/obo/CL_0000623` +#### Removed +- [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009278"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009278"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neocortex basket cell `http://purl.obolibrary.org/obo/CL_2000086` +#### Removed +- [neocortex basket cell](http://purl.obolibrary.org/obo/CL_2000086) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [neocortex basket cell](http://purl.obolibrary.org/obo/CL_2000086) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### nephrogenic mesenchyme stem cell `http://purl.obolibrary.org/obo/CL_0000383` +#### Removed +- [nephrogenic mesenchyme stem cell](http://purl.obolibrary.org/obo/CL_0000383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009187"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [nephrogenic mesenchyme stem cell](http://purl.obolibrary.org/obo/CL_0000383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009187"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neural crest derived neuron `http://purl.obolibrary.org/obo/CL_0000029` +#### Removed +- [neural crest derived neuron](http://purl.obolibrary.org/obo/CL_0000029) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009009"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neural crest derived neuron](http://purl.obolibrary.org/obo/CL_0000029) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009009"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neural stem cell `http://purl.obolibrary.org/obo/CL_0000047` +#### Removed +- [neural stem cell](http://purl.obolibrary.org/obo/CL_0000047) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009019"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neural stem cell](http://purl.obolibrary.org/obo/CL_0000047) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009019"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neurectodermal cell `http://purl.obolibrary.org/obo/CL_0000133` +#### Removed +- [neurectodermal cell](http://purl.obolibrary.org/obo/CL_0000133) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009080"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neurectodermal cell](http://purl.obolibrary.org/obo/CL_0000133) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009080"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000338` +#### Removed +- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005146"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005146"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000031` +#### Removed +- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroendocrine cell `http://purl.obolibrary.org/obo/CL_0000165` +#### Removed +- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009098"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005130"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005130"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009098"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroendocrine cell of epithelium of lobar bronchus `http://purl.obolibrary.org/obo/CL_4033010` + +#### Added +- [neuroendocrine cell of epithelium of lobar bronchus](http://purl.obolibrary.org/obo/CL_4033010) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + +### neurogliaform cell `http://purl.obolibrary.org/obo/CL_0000693` +#### Removed +- [neurogliaform cell](http://purl.obolibrary.org/obo/CL_0000693) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009299"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neurogliaform cell](http://purl.obolibrary.org/obo/CL_0000693) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009299"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroglioblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000468` +#### Removed +- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005147"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005147"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuromast hair cell `http://purl.obolibrary.org/obo/CL_0000856` +#### Removed +- [neuromast hair cell](http://purl.obolibrary.org/obo/CL_0000856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009367"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuromast hair cell](http://purl.obolibrary.org/obo/CL_0000856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009367"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuromast mantle cell `http://purl.obolibrary.org/obo/CL_0000851` +#### Removed +- [neuromast mantle cell](http://purl.obolibrary.org/obo/CL_0000851) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009362"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuromast mantle cell](http://purl.obolibrary.org/obo/CL_0000851) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009362"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuromast supporting cell `http://purl.obolibrary.org/obo/CL_0000852` +#### Removed +- [neuromast supporting cell](http://purl.obolibrary.org/obo/CL_0000852) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009363"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuromast supporting cell](http://purl.obolibrary.org/obo/CL_0000852) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009363"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuron `http://purl.obolibrary.org/obo/CL_0000540` +#### Removed +- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009248"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005106"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005106"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009248"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuronal receptor cell `http://purl.obolibrary.org/obo/CL_0000006` +#### Removed +- [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009001"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009001"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neuroplacodal cell `http://purl.obolibrary.org/obo/CL_0000032` +#### Removed +- [neuroplacodal cell](http://purl.obolibrary.org/obo/CL_0000032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009012"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neuroplacodal cell](http://purl.obolibrary.org/obo/CL_0000032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009012"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neutrophil `http://purl.obolibrary.org/obo/CL_0000775` +#### Removed +- [neutrophil](http://purl.obolibrary.org/obo/CL_0000775) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009327"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neutrophil](http://purl.obolibrary.org/obo/CL_0000775) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009327"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neutrophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000834` +#### Removed +- [neutrophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000834) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009352"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neutrophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000834) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009352"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neutrophilic metamyelocyte `http://purl.obolibrary.org/obo/CL_0000582` +#### Removed +- [neutrophilic metamyelocyte](http://purl.obolibrary.org/obo/CL_0000582) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009268"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neutrophilic metamyelocyte](http://purl.obolibrary.org/obo/CL_0000582) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009268"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neutrophilic myeloblast `http://purl.obolibrary.org/obo/CL_0000042` +#### Removed +- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009018"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009018"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neutrophilic myelocyte `http://purl.obolibrary.org/obo/CL_0000580` +#### Removed +- [neutrophilic myelocyte](http://purl.obolibrary.org/obo/CL_0000580) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009266"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neutrophilic myelocyte](http://purl.obolibrary.org/obo/CL_0000580) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009266"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### neutrophilic promyelocyte `http://purl.obolibrary.org/obo/CL_0000564` +#### Removed +- [neutrophilic promyelocyte](http://purl.obolibrary.org/obo/CL_0000564) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009257"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [neutrophilic promyelocyte](http://purl.obolibrary.org/obo/CL_0000564) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009257"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### nitrergic neuron `http://purl.obolibrary.org/obo/CL_0000528` +#### Removed +- [nitrergic neuron](http://purl.obolibrary.org/obo/CL_0000528) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009240"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [nitrergic neuron](http://purl.obolibrary.org/obo/CL_0000528) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009240"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### noradrenergic cell `http://purl.obolibrary.org/obo/CL_0000459` +#### Removed +- [noradrenergic cell](http://purl.obolibrary.org/obo/CL_0000459) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009214"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [noradrenergic cell](http://purl.obolibrary.org/obo/CL_0000459) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009214"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### noradrenergic neuron `http://purl.obolibrary.org/obo/CL_0008025` +#### Removed +- [noradrenergic neuron](http://purl.obolibrary.org/obo/CL_0008025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005873"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [noradrenergic neuron](http://purl.obolibrary.org/obo/CL_0008025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005873"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### notochordal sheath cell `http://purl.obolibrary.org/obo/CL_0007007` +#### Removed +- [notochordal sheath cell](http://purl.obolibrary.org/obo/CL_0007007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005744"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [notochordal sheath cell](http://purl.obolibrary.org/obo/CL_0007007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005744"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### nucleate erythrocyte `http://purl.obolibrary.org/obo/CL_0000562` +#### Removed +- [nucleate erythrocyte](http://purl.obolibrary.org/obo/CL_0000562) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009256"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [nucleate erythrocyte](http://purl.obolibrary.org/obo/CL_0000562) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009256"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### nucleated thrombocyte `http://purl.obolibrary.org/obo/CL_0000762` +#### Removed +- [nucleated thrombocyte](http://purl.obolibrary.org/obo/CL_0000762) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009323"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [nucleated thrombocyte](http://purl.obolibrary.org/obo/CL_0000762) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009323"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### obsolete cerebellum Golgi cell `http://purl.obolibrary.org/obo/CL_2000026` +#### Removed +- [obsolete cerebellum Golgi cell](http://purl.obolibrary.org/obo/CL_2000026) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [obsolete cerebellum Golgi cell](http://purl.obolibrary.org/obo/CL_2000026) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### obsolete melanocyte of foreskin `http://purl.obolibrary.org/obo/CL_2000082` +#### Removed +- [obsolete melanocyte of foreskin](http://purl.obolibrary.org/obo/CL_2000082) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [obsolete melanocyte of foreskin](http://purl.obolibrary.org/obo/CL_2000082) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### obsolete microvascular endothelium blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000009` +#### Removed +- [obsolete microvascular endothelium blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000009) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [obsolete microvascular endothelium blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000009) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### obsolete retina retinal ganglion cell `http://purl.obolibrary.org/obo/CL_2000050` +#### Removed +- [obsolete retina retinal ganglion cell](http://purl.obolibrary.org/obo/CL_2000050) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [obsolete retina retinal ganglion cell](http://purl.obolibrary.org/obo/CL_2000050) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### odontoblast `http://purl.obolibrary.org/obo/CL_0000060` +#### Removed +- [odontoblast](http://purl.obolibrary.org/obo/CL_0000060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009029"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [odontoblast](http://purl.obolibrary.org/obo/CL_0000060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009029"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### odontoclast `http://purl.obolibrary.org/obo/CL_0000588` +#### Removed +- [odontoclast](http://purl.obolibrary.org/obo/CL_0000588) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009270"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [odontoclast](http://purl.obolibrary.org/obo/CL_0000588) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009270"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### odontocyte `http://purl.obolibrary.org/obo/CL_0000140` +#### Removed +- [odontocyte](http://purl.obolibrary.org/obo/CL_0000140) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009086"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [odontocyte](http://purl.obolibrary.org/obo/CL_0000140) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009086"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### oenocyte `http://purl.obolibrary.org/obo/CL_0000487` +#### Removed +- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004995"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004995"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### olfactory ensheathing cell `http://purl.obolibrary.org/obo/CL_0011028` +#### Removed +- [olfactory ensheathing cell](http://purl.obolibrary.org/obo/CL_0011028) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22456085"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [olfactory ensheathing cell](http://purl.obolibrary.org/obo/CL_0011028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22456085"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### olfactory epithelial supporting cell `http://purl.obolibrary.org/obo/CL_0000853` +#### Removed +- [olfactory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0000853) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009364"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [olfactory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0000853) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009364"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### olfactory granule cell `http://purl.obolibrary.org/obo/CL_0000626` +#### Removed +- [olfactory granule cell](http://purl.obolibrary.org/obo/CL_0000626) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001694"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [olfactory granule cell](http://purl.obolibrary.org/obo/CL_0000626) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001694"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### olfactory receptor cell `http://purl.obolibrary.org/obo/CL_0000207` +#### Removed +- [olfactory receptor cell](http://purl.obolibrary.org/obo/CL_0000207) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009125"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [olfactory receptor cell](http://purl.obolibrary.org/obo/CL_0000207) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009125"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### oligodendrocyte `http://purl.obolibrary.org/obo/CL_0000128` +#### Removed +- [oligodendrocyte](http://purl.obolibrary.org/obo/CL_0000128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009076"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [oligodendrocyte](http://purl.obolibrary.org/obo/CL_0000128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009076"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### oocyte `http://purl.obolibrary.org/obo/CL_0000023` +#### Removed +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004886"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001109"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001109"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004886"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### oogonial cell `http://purl.obolibrary.org/obo/CL_0000024` +#### Removed +- [oogonial cell](http://purl.obolibrary.org/obo/CL_0000024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005878"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [oogonial cell](http://purl.obolibrary.org/obo/CL_0000024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005878"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### open tracheal system tracheocyte `http://purl.obolibrary.org/obo/CL_0008026` +#### Removed +- [open tracheal system tracheocyte](http://purl.obolibrary.org/obo/CL_0008026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005038"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [open tracheal system tracheocyte](http://purl.obolibrary.org/obo/CL_0008026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005038"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### optic choroid fibroblast `http://purl.obolibrary.org/obo/CL_2000070` +#### Removed +- [optic choroid fibroblast](http://purl.obolibrary.org/obo/CL_2000070) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [optic choroid fibroblast](http://purl.obolibrary.org/obo/CL_2000070) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### osteoblast `http://purl.obolibrary.org/obo/CL_0000062` +#### Removed +- [osteoblast](http://purl.obolibrary.org/obo/CL_0000062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009031"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [osteoblast](http://purl.obolibrary.org/obo/CL_0000062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009031"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### osteoclast `http://purl.obolibrary.org/obo/CL_0000092` +#### Removed +- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009047"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009047"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### osteocyte `http://purl.obolibrary.org/obo/CL_0000137` +#### Removed +- [osteocyte](http://purl.obolibrary.org/obo/CL_0000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009083"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [osteocyte](http://purl.obolibrary.org/obo/CL_0000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009083"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ovarian fibroblast `http://purl.obolibrary.org/obo/CL_2000063` +#### Removed +- [ovarian fibroblast](http://purl.obolibrary.org/obo/CL_2000063) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [ovarian fibroblast](http://purl.obolibrary.org/obo/CL_2000063) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### ovarian microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000065` +#### Removed +- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) SubClassOf [epithelial cell of urethra](http://purl.obolibrary.org/obo/CL_1000296) + +#### Added +- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + +- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) SubClassOf [urethra cell](http://purl.obolibrary.org/obo/CL_1001320) + + +### ovarian surface epithelial cell `http://purl.obolibrary.org/obo/CL_2000064` +#### Removed +- [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### oxygen accumulating cell `http://purl.obolibrary.org/obo/CL_0000329` +#### Removed +- [oxygen accumulating cell](http://purl.obolibrary.org/obo/CL_0000329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009164"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [oxygen accumulating cell](http://purl.obolibrary.org/obo/CL_0000329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009164"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pain receptor cell `http://purl.obolibrary.org/obo/CL_0000198` +#### Removed +- [pain receptor cell](http://purl.obolibrary.org/obo/CL_0000198) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009119"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pain receptor cell](http://purl.obolibrary.org/obo/CL_0000198) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009119"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic A cell `http://purl.obolibrary.org/obo/CL_0000171` +#### Removed +- [pancreatic A cell](http://purl.obolibrary.org/obo/CL_0000171) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009104"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic A cell](http://purl.obolibrary.org/obo/CL_0000171) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009104"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic D cell `http://purl.obolibrary.org/obo/CL_0000173` +#### Removed +- [pancreatic D cell](http://purl.obolibrary.org/obo/CL_0000173) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005743"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic D cell](http://purl.obolibrary.org/obo/CL_0000173) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005743"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic PP cell `http://purl.obolibrary.org/obo/CL_0002275` +#### Removed +- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005742"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005742"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic acinar cell `http://purl.obolibrary.org/obo/CL_0002064` +#### Removed +- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005739"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005739"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic centro-acinar cell `http://purl.obolibrary.org/obo/CL_0002080` +#### Removed +- [pancreatic centro-acinar cell](http://purl.obolibrary.org/obo/CL_0002080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005740"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic centro-acinar cell](http://purl.obolibrary.org/obo/CL_0002080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005740"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic ductal cell `http://purl.obolibrary.org/obo/CL_0002079` +#### Removed +- [pancreatic ductal cell](http://purl.obolibrary.org/obo/CL_0002079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009380"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic ductal cell](http://purl.obolibrary.org/obo/CL_0002079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009380"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pancreatic epsilon cell `http://purl.obolibrary.org/obo/CL_0005019` +#### Removed +- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005598"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005598"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### paracrine cell `http://purl.obolibrary.org/obo/CL_0000512` +#### Removed +- [paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009233"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009233"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### parafollicular cell `http://purl.obolibrary.org/obo/CL_0000570` +#### Removed +- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009260"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009260"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### parasympathetic neuron `http://purl.obolibrary.org/obo/CL_0011102` +#### Removed +- [parasympathetic neuron](http://purl.obolibrary.org/obo/CL_0011102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005776"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [parasympathetic neuron](http://purl.obolibrary.org/obo/CL_0011102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005776"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### peptide hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000167` +#### Removed +- [peptide hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000167) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009100"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [peptide hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000167) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009100"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### peptidergic neuron `http://purl.obolibrary.org/obo/CL_0000110` +#### Removed +- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009062"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004101"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009062"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004101"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### periarticular chondrocyte `http://purl.obolibrary.org/obo/CL_0000742` +#### Removed +- [periarticular chondrocyte](http://purl.obolibrary.org/obo/CL_0000742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009312"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [periarticular chondrocyte](http://purl.obolibrary.org/obo/CL_0000742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009312"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pericardial nephrocyte `http://purl.obolibrary.org/obo/CL_0000474` +#### Removed +- [pericardial nephrocyte](http://purl.obolibrary.org/obo/CL_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005058"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pericardial nephrocyte](http://purl.obolibrary.org/obo/CL_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005058"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pericardium fibroblast `http://purl.obolibrary.org/obo/CL_2000068` +#### Removed +- [pericardium fibroblast](http://purl.obolibrary.org/obo/CL_2000068) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [pericardium fibroblast](http://purl.obolibrary.org/obo/CL_2000068) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### pericyte `http://purl.obolibrary.org/obo/CL_0000669` +#### Removed +- [pericyte](http://purl.obolibrary.org/obo/CL_0000669) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009112"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pericyte](http://purl.obolibrary.org/obo/CL_0000669) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009112"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### peridermal cell `http://purl.obolibrary.org/obo/CL_0000078` +#### Removed +- [peridermal cell](http://purl.obolibrary.org/obo/CL_0000078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009041"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [peridermal cell](http://purl.obolibrary.org/obo/CL_0000078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009041"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### perijunctional fibroblast `http://purl.obolibrary.org/obo/CL_0000688` +#### Removed +- [perijunctional fibroblast](http://purl.obolibrary.org/obo/CL_0000688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009296"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [perijunctional fibroblast](http://purl.obolibrary.org/obo/CL_0000688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009296"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### perineuronal satellite cell `http://purl.obolibrary.org/obo/CL_0000516` +#### Removed +- [perineuronal satellite cell](http://purl.obolibrary.org/obo/CL_0000516) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009237"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [perineuronal satellite cell](http://purl.obolibrary.org/obo/CL_0000516) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009237"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### peripheral blood mononuclear cell `http://purl.obolibrary.org/obo/CL_2000001` +#### Removed +- [peripheral blood mononuclear cell](http://purl.obolibrary.org/obo/CL_2000001) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [peripheral blood mononuclear cell](http://purl.obolibrary.org/obo/CL_2000001) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### peripheral nervous system neuron `http://purl.obolibrary.org/obo/CL_2000032` +#### Removed +- [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### peripheral sensory neuron `http://purl.obolibrary.org/obo/CL_3000004` +#### Removed +- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) + +#### Added +- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) + + +### peritoneal macrophage `http://purl.obolibrary.org/obo/CL_0000581` +#### Removed +- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009267"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009267"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### phagocyte `http://purl.obolibrary.org/obo/CL_0000234` +#### Removed +- [phagocyte](http://purl.obolibrary.org/obo/CL_0000234) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009140"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [phagocyte](http://purl.obolibrary.org/obo/CL_0000234) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009140"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### photopic photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000490` +#### Removed +- [photopic photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000490) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009220"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [photopic photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000490) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009220"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000210` +#### Removed +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004211"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009127"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004211"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009127"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pigment cell `http://purl.obolibrary.org/obo/CL_0000147` +#### Removed +- [pigment cell](http://purl.obolibrary.org/obo/CL_0000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009090"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pigment cell](http://purl.obolibrary.org/obo/CL_0000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009090"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pigment cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000342` +#### Removed +- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009170"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009170"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pigment erythroblast `http://purl.obolibrary.org/obo/CL_0005004` +#### Removed +- [pigment erythroblast](http://purl.obolibrary.org/obo/CL_0005004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005331"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pigment erythroblast](http://purl.obolibrary.org/obo/CL_0005004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005331"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pigmented epithelial cell `http://purl.obolibrary.org/obo/CL_0000529` +#### Removed +- [pigmented epithelial cell](http://purl.obolibrary.org/obo/CL_0000529) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009241"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pigmented epithelial cell](http://purl.obolibrary.org/obo/CL_0000529) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009241"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pinealocyte `http://purl.obolibrary.org/obo/CL_0000652` +#### Removed +- [pinealocyte](http://purl.obolibrary.org/obo/CL_0000652) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009284"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pinealocyte](http://purl.obolibrary.org/obo/CL_0000652) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009284"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pioneer neuron `http://purl.obolibrary.org/obo/CL_0000116` +#### Removed +- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009066"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005128"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005128"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009066"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pituitary gland cell `http://purl.obolibrary.org/obo/CL_2000004` +#### Removed +- [pituitary gland cell](http://purl.obolibrary.org/obo/CL_2000004) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [pituitary gland cell](http://purl.obolibrary.org/obo/CL_2000004) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### placental amniotic mesenchymal stromal cell `http://purl.obolibrary.org/obo/CL_2000061` +#### Removed +- [placental amniotic mesenchymal stromal cell](http://purl.obolibrary.org/obo/CL_2000061) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [placental amniotic mesenchymal stromal cell](http://purl.obolibrary.org/obo/CL_2000061) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### placental pericyte `http://purl.obolibrary.org/obo/CL_2000078` +#### Removed +- [placental pericyte](http://purl.obolibrary.org/obo/CL_2000078) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [placental pericyte](http://purl.obolibrary.org/obo/CL_2000078) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### placental villous trophoblast `http://purl.obolibrary.org/obo/CL_2000060` +#### Removed +- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### placental villus capillary endothelial cell `http://purl.obolibrary.org/obo/CL_2000062` +#### Removed +- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### plasma cell `http://purl.obolibrary.org/obo/CL_0000786` +#### Removed +- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009332"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009332"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### plasmatocyte `http://purl.obolibrary.org/obo/CL_0000394` +#### Removed +- [plasmatocyte](http://purl.obolibrary.org/obo/CL_0000394) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001685"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [plasmatocyte](http://purl.obolibrary.org/obo/CL_0000394) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001685"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pneumocyte `http://purl.obolibrary.org/obo/CL_0000322` +#### Removed +- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) [label](http://www.w3.org/2000/01/rdf-schema#label) "pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29463737"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary alveolar epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32491474"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + + +### podocyte `http://purl.obolibrary.org/obo/CL_0000653` +#### Removed +- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009285"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009285"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pole cell `http://purl.obolibrary.org/obo/CL_0000301` +#### Removed +- [pole cell](http://purl.obolibrary.org/obo/CL_0000301) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000092"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pole cell](http://purl.obolibrary.org/obo/CL_0000301) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000092"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### polychromatophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000550` +#### Removed +- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005241"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005241"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### polymodal neuron `http://purl.obolibrary.org/obo/CL_0000102` +#### Removed +- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009054"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009054"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### posterior lateral line neuromast hair cell `http://purl.obolibrary.org/obo/CL_2000037` +#### Removed +- [posterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000037) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [posterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000037) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### posterior lateral line neuromast mantle cell `http://purl.obolibrary.org/obo/CL_2000038` +#### Removed +- [posterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000038) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [posterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000038) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### posterior lateral line neuromast supporting cell `http://purl.obolibrary.org/obo/CL_2000039` +#### Removed +- [posterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000039) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [posterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000039) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### pre-granulosa cell `http://purl.obolibrary.org/obo/CL_4033066` + +#### Added +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033066"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [date](http://purl.org/dc/terms/date) "2024-06-07T12:04:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pregranulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17639032"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PG cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ovarian pregranulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [label](http://www.w3.org/2000/01/rdf-schema#label) "pre-granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17639032"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38178246"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000992](http://purl.obolibrary.org/obo/UBERON_0000992) + +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) + + +### precursor B cell `http://purl.obolibrary.org/obo/CL_0000817` +#### Removed +- [precursor B cell](http://purl.obolibrary.org/obo/CL_0000817) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009344"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [precursor B cell](http://purl.obolibrary.org/obo/CL_0000817) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009344"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### premigratory neural crest cell `http://purl.obolibrary.org/obo/CL_0007004` +#### Removed +- [premigratory neural crest cell](http://purl.obolibrary.org/obo/CL_0007004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [premigratory neural crest cell](http://purl.obolibrary.org/obo/CL_0007004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pressoreceptor cell `http://purl.obolibrary.org/obo/CL_0000602` +#### Removed +- [pressoreceptor cell](http://purl.obolibrary.org/obo/CL_0000602) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009274"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pressoreceptor cell](http://purl.obolibrary.org/obo/CL_0000602) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009274"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### primary interneuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000534` +#### Removed +- [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009245"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009245"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### primary motor cortex pyramidal cell `http://purl.obolibrary.org/obo/CL_2000049` +#### Removed +- [primary motor cortex pyramidal cell](http://purl.obolibrary.org/obo/CL_2000049) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [primary motor cortex pyramidal cell](http://purl.obolibrary.org/obo/CL_2000049) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### primary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000533` +#### Removed +- [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009244"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009244"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` +#### Removed +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009242"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009242"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### primordial germ cell `http://purl.obolibrary.org/obo/CL_0000670` +#### Removed +- [primordial germ cell](http://purl.obolibrary.org/obo/CL_0000670) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009288"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [primordial germ cell](http://purl.obolibrary.org/obo/CL_0000670) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009288"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pro-B cell `http://purl.obolibrary.org/obo/CL_0000826` +#### Removed +- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009349"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009349"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pro-NK cell `http://purl.obolibrary.org/obo/CL_0000825` +#### Removed +- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009348"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009348"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pro-T cell `http://purl.obolibrary.org/obo/CL_0000827` +#### Removed +- [pro-T cell](http://purl.obolibrary.org/obo/CL_0000827) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009350"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pro-T cell](http://purl.obolibrary.org/obo/CL_0000827) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009350"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### procrystal cell `http://purl.obolibrary.org/obo/CL_0000395` +#### Removed +- [procrystal cell](http://purl.obolibrary.org/obo/CL_0000395) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001689"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [procrystal cell](http://purl.obolibrary.org/obo/CL_0000395) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001689"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### professional antigen presenting cell `http://purl.obolibrary.org/obo/CL_0000145` +#### Removed +- [professional antigen presenting cell](http://purl.obolibrary.org/obo/CL_0000145) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009088"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [professional antigen presenting cell](http://purl.obolibrary.org/obo/CL_0000145) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009088"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### progesterone secreting cell `http://purl.obolibrary.org/obo/CL_0000179` +#### Removed +- [progesterone secreting cell](http://purl.obolibrary.org/obo/CL_0000179) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009109"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [progesterone secreting cell](http://purl.obolibrary.org/obo/CL_0000179) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009109"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### prohemocyte (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000385` +#### Removed +- [prohemocyte (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000385) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005062"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [prohemocyte (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000385) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005062"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### prolactin secreting cell `http://purl.obolibrary.org/obo/CL_0000439` +#### Removed +- [prolactin secreting cell](http://purl.obolibrary.org/obo/CL_0000439) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009204"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [prolactin secreting cell](http://purl.obolibrary.org/obo/CL_0000439) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009204"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### promonocyte `http://purl.obolibrary.org/obo/CL_0000559` +#### Removed +- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009253"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009253"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### prostate gland microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000059` +#### Removed +- [prostate gland microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000059) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [prostate gland microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000059) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### pseudounipolar neuron `http://purl.obolibrary.org/obo/CL_0000105` +#### Removed +- [pseudounipolar neuron](http://purl.obolibrary.org/obo/CL_0000105) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009057"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pseudounipolar neuron](http://purl.obolibrary.org/obo/CL_0000105) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009057"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### pulmonary ionocyte `http://purl.obolibrary.org/obo/CL_0017000` + +#### Added +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) EquivalentTo [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) + + +### pyramidal neuron `http://purl.obolibrary.org/obo/CL_0000598` +#### Removed +- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009273"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009273"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### radial glial cell `http://purl.obolibrary.org/obo/CL_0000681` +#### Removed +- [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009292"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009292"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### red sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000497` +#### Removed +- [red sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009224"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [red sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009224"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### renal alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_0005011` +#### Removed +- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009376"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009376"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### renal intercalated cell `http://purl.obolibrary.org/obo/CL_0005010` +#### Removed +- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009375"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009375"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### renal principal cell `http://purl.obolibrary.org/obo/CL_0005009` +#### Removed +- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005322"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005322"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### respiratory basal cell `http://purl.obolibrary.org/obo/CL_0002633` +#### Removed +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + +#### Added +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) EquivalentTo [basal cell](http://purl.obolibrary.org/obo/CL_0000646) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) + +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + + +### respiratory epithelial cell `http://purl.obolibrary.org/obo/CL_0002368` +#### Removed +- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) EquivalentTo [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065)) + +- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065) + +- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) + +- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) + +- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + + +### respiratory goblet cell `http://purl.obolibrary.org/obo/CL_0002370` +#### Removed +- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065)) + +- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + +#### Added +- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) + +- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) + + +### respiratory hillock cell `http://purl.obolibrary.org/obo/CL_4030023` +#### Removed +- [respiratory hillock cell](http://purl.obolibrary.org/obo/CL_4030023) EquivalentTo [hillock cell](http://purl.obolibrary.org/obo/CL_4030024) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065)) + +#### Added +- [respiratory hillock cell](http://purl.obolibrary.org/obo/CL_4030023) EquivalentTo [hillock cell](http://purl.obolibrary.org/obo/CL_4030024) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) + + +### respiratory suprabasal cell `http://purl.obolibrary.org/obo/CL_4033048` +#### Removed +- [respiratory suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + + + +### reticular cell `http://purl.obolibrary.org/obo/CL_0000432` +#### Removed +- [reticular cell](http://purl.obolibrary.org/obo/CL_0000432) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009200"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [reticular cell](http://purl.obolibrary.org/obo/CL_0000432) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009200"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### reticulocyte `http://purl.obolibrary.org/obo/CL_0000558` +#### Removed +- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009252"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009252"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### retina horizontal cell `http://purl.obolibrary.org/obo/CL_0000745` +#### Removed +- [retina horizontal cell](http://purl.obolibrary.org/obo/CL_0000745) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009315"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [retina horizontal cell](http://purl.obolibrary.org/obo/CL_0000745) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009315"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### retinal bipolar neuron `http://purl.obolibrary.org/obo/CL_0000748` +#### Removed +- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009318"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009318"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### retinal cone cell `http://purl.obolibrary.org/obo/CL_0000573` +#### Removed +- [retinal cone cell](http://purl.obolibrary.org/obo/CL_0000573) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009262"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [retinal cone cell](http://purl.obolibrary.org/obo/CL_0000573) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009262"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### retinal ganglion cell `http://purl.obolibrary.org/obo/CL_0000740` +#### Removed +- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009310"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009310"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### retinal rod cell `http://purl.obolibrary.org/obo/CL_0000604` +#### Removed +- [retinal rod cell](http://purl.obolibrary.org/obo/CL_0000604) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009275"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [retinal rod cell](http://purl.obolibrary.org/obo/CL_0000604) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009275"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### rod bipolar cell `http://purl.obolibrary.org/obo/CL_0000751` +#### Removed +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009321"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009321"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### scleral cell `http://purl.obolibrary.org/obo/CL_0000347` +#### Removed +- [scleral cell](http://purl.obolibrary.org/obo/CL_0000347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009174"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [scleral cell](http://purl.obolibrary.org/obo/CL_0000347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009174"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### scolopale cell `http://purl.obolibrary.org/obo/CL_0000382` +#### Removed +- [scolopale cell](http://purl.obolibrary.org/obo/CL_0000382) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [scolopale cell](http://purl.obolibrary.org/obo/CL_0000382) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### scolopidial ligament cell `http://purl.obolibrary.org/obo/CL_0000407` +#### Removed +- [scolopidial ligament cell](http://purl.obolibrary.org/obo/CL_0000407) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [scolopidial ligament cell](http://purl.obolibrary.org/obo/CL_0000407) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sebaceous gland cell `http://purl.obolibrary.org/obo/CL_2000021` +#### Removed +- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### secondary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000536` +#### Removed +- [secondary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009247"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [secondary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009247"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` +#### Removed +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009246"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009246"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### secondary spermatocyte `http://purl.obolibrary.org/obo/CL_0000657` +#### Removed +- [secondary spermatocyte](http://purl.obolibrary.org/obo/CL_0000657) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004941"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [secondary spermatocyte](http://purl.obolibrary.org/obo/CL_0000657) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004941"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sensory epithelial cell `http://purl.obolibrary.org/obo/CL_0000098` +#### Removed +- [sensory epithelial cell](http://purl.obolibrary.org/obo/CL_0000098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009050"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sensory epithelial cell](http://purl.obolibrary.org/obo/CL_0000098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009050"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sensory hair cell `http://purl.obolibrary.org/obo/CL_0000855` +#### Removed +- [sensory hair cell](http://purl.obolibrary.org/obo/CL_0000855) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009366"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sensory hair cell](http://purl.obolibrary.org/obo/CL_0000855) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009366"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sensory neuron `http://purl.obolibrary.org/obo/CL_0000101` +#### Removed +- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005124"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009053"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005124"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009053"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sensory processing neuron `http://purl.obolibrary.org/obo/CL_0000379` +#### Removed +- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009185"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009185"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### serotonergic neuron `http://purl.obolibrary.org/obo/CL_0000850` +#### Removed +- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009361"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005133"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005133"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009361"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### serotonin secreting cell `http://purl.obolibrary.org/obo/CL_0000458` +#### Removed +- [serotonin secreting cell](http://purl.obolibrary.org/obo/CL_0000458) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009213"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [serotonin secreting cell](http://purl.obolibrary.org/obo/CL_0000458) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009213"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### simple columnar epithelial cell `http://purl.obolibrary.org/obo/CL_0000146` +#### Removed +- [simple columnar epithelial cell](http://purl.obolibrary.org/obo/CL_0000146) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009089"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [simple columnar epithelial cell](http://purl.obolibrary.org/obo/CL_0000146) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009089"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### single ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005013` +#### Removed +- [single ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005013) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005243"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [single ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005013) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005243"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### single fate stem cell `http://purl.obolibrary.org/obo/CL_0000035` +#### Removed +- [single fate stem cell](http://purl.obolibrary.org/obo/CL_0000035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009013"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [single fate stem cell](http://purl.obolibrary.org/obo/CL_0000035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009013"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### skeletal muscle myoblast `http://purl.obolibrary.org/obo/CL_0000515` +#### Removed +- [skeletal muscle myoblast](http://purl.obolibrary.org/obo/CL_0000515) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009236"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [skeletal muscle myoblast](http://purl.obolibrary.org/obo/CL_0000515) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009236"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### skeletal muscle satellite cell `http://purl.obolibrary.org/obo/CL_0000594` +#### Removed +- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009272"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009272"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### skeletal muscle tissue of pectoralis major striated muscle cell `http://purl.obolibrary.org/obo/CL_2000077` +#### Removed +- [skeletal muscle tissue of pectoralis major striated muscle cell](http://purl.obolibrary.org/obo/CL_2000077) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [skeletal muscle tissue of pectoralis major striated muscle cell](http://purl.obolibrary.org/obo/CL_2000077) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### slow muscle cell `http://purl.obolibrary.org/obo/CL_0000189` +#### Removed +- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009116"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009116"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### slow muscle myoblast `http://purl.obolibrary.org/obo/CL_0000857` +#### Removed +- [slow muscle myoblast](http://purl.obolibrary.org/obo/CL_0000857) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009368"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [slow muscle myoblast](http://purl.obolibrary.org/obo/CL_0000857) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009368"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000192` +#### Removed +- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009118"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009118"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### smooth muscle myoblast `http://purl.obolibrary.org/obo/CL_0000514` +#### Removed +- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009235"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009235"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sncg GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023015` +#### Removed +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + +#### Added +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) + + +### somatic muscle cell `http://purl.obolibrary.org/obo/CL_0008004` +#### Removed +- [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005073"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005073"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### somatic stem cell `http://purl.obolibrary.org/obo/CL_0000723` +#### Removed +- [somatic stem cell](http://purl.obolibrary.org/obo/CL_0000723) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009307"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [somatic stem cell](http://purl.obolibrary.org/obo/CL_0000723) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009307"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### somatomotor neuron `http://purl.obolibrary.org/obo/CL_0005024` +#### Removed +- [somatomotor neuron](http://purl.obolibrary.org/obo/CL_0005024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005733"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [somatomotor neuron](http://purl.obolibrary.org/obo/CL_0005024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005733"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### somatostatin secreting cell `http://purl.obolibrary.org/obo/CL_0000172` +#### Removed +- [somatostatin secreting cell](http://purl.obolibrary.org/obo/CL_0000172) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009105"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [somatostatin secreting cell](http://purl.obolibrary.org/obo/CL_0000172) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009105"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### somatotropin secreting cell `http://purl.obolibrary.org/obo/CL_0000295` +#### Removed +- [somatotropin secreting cell](http://purl.obolibrary.org/obo/CL_0000295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009155"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [somatotropin secreting cell](http://purl.obolibrary.org/obo/CL_0000295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009155"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sperm `http://purl.obolibrary.org/obo/CL_0000019` +#### Removed +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004954"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009006"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004954"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009006"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### spermatid `http://purl.obolibrary.org/obo/CL_0000018` +#### Removed +- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004942"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005769"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004942"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005769"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### spermatocyte `http://purl.obolibrary.org/obo/CL_0000017` +#### Removed +- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004936"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009005"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004936"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009005"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### spermatogonium `http://purl.obolibrary.org/obo/CL_0000020` +#### Removed +- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004934"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009007"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004935"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004935"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009007"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004934"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### spinal accessory motor neuron `http://purl.obolibrary.org/obo/CL_0000741` +#### Removed +- [spinal accessory motor neuron](http://purl.obolibrary.org/obo/CL_0000741) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009311"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [spinal accessory motor neuron](http://purl.obolibrary.org/obo/CL_0000741) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009311"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### spinal cord interneuron `http://purl.obolibrary.org/obo/CL_0005000` +#### Removed +- [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000778"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000778"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### spinal cord medial motor column neuron `http://purl.obolibrary.org/obo/CL_2000024` +#### Removed +- [spinal cord medial motor column neuron](http://purl.obolibrary.org/obo/CL_2000024) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [spinal cord medial motor column neuron](http://purl.obolibrary.org/obo/CL_2000024) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### spinal cord oligodendrocyte `http://purl.obolibrary.org/obo/CL_2000025` +#### Removed +- [spinal cord oligodendrocyte](http://purl.obolibrary.org/obo/CL_2000025) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [spinal cord oligodendrocyte](http://purl.obolibrary.org/obo/CL_2000025) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### spinal cord ventral column interneuron `http://purl.obolibrary.org/obo/CL_2000023` +#### Removed +- [spinal cord ventral column interneuron](http://purl.obolibrary.org/obo/CL_2000023) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [spinal cord ventral column interneuron](http://purl.obolibrary.org/obo/CL_2000023) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### splenic endothelial cell `http://purl.obolibrary.org/obo/CL_2000053` +#### Removed +- [splenic endothelial cell](http://purl.obolibrary.org/obo/CL_2000053) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [splenic endothelial cell](http://purl.obolibrary.org/obo/CL_2000053) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### splenic fibroblast `http://purl.obolibrary.org/obo/CL_2000051` +#### Removed +- [splenic fibroblast](http://purl.obolibrary.org/obo/CL_2000051) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [splenic fibroblast](http://purl.obolibrary.org/obo/CL_2000051) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### splenocyte `http://purl.obolibrary.org/obo/CL_2000074` +#### Removed +- [splenocyte](http://purl.obolibrary.org/obo/CL_2000074) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [splenocyte](http://purl.obolibrary.org/obo/CL_2000074) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### squamous endothelial cell `http://purl.obolibrary.org/obo/CL_0002653` +#### Removed +- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) + +- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) SubClassOf [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) + +#### Added +- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A squamous shaped endothelial cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + + +### squamous endothelial cell of venule `http://purl.obolibrary.org/obo/CL_0008040` + +#### Added +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [date](http://purl.org/dc/elements/1.1/date) "2024-07-03T19:52:47Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:0008040"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [label](http://www.w3.org/2000/01/rdf-schema#label) "squamous endothelial cell of venule"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) + +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) SubClassOf [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) + +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) SubClassOf [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) + + +### squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000076` +#### Removed +- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009039"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009039"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stellate interneuron `http://purl.obolibrary.org/obo/CL_0000691` +#### Removed +- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009297"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009297"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stellate neuron `http://purl.obolibrary.org/obo/CL_0000122` +#### Removed +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009072"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009072"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stem cell `http://purl.obolibrary.org/obo/CL_0000034` +#### Removed +- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005957"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005957"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stem cell of epidermis `http://purl.obolibrary.org/obo/CL_1000428` +#### Removed +- [stem cell of epidermis](http://purl.obolibrary.org/obo/CL_1000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007122"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stem cell of epidermis](http://purl.obolibrary.org/obo/CL_1000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007122"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### steroid hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000174` +#### Removed +- [steroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000174) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009106"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [steroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000174) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009106"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stratified cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000241` +#### Removed +- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009145"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009145"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stratified epithelial cell `http://purl.obolibrary.org/obo/CL_0000079` +#### Removed +- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009042"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009042"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stratified epithelial stem cell `http://purl.obolibrary.org/obo/CL_0000357` +#### Removed +- [stratified epithelial stem cell](http://purl.obolibrary.org/obo/CL_0000357) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009180"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stratified epithelial stem cell](http://purl.obolibrary.org/obo/CL_0000357) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009180"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stratified keratinized epithelial stem cell `http://purl.obolibrary.org/obo/CL_1000083` +#### Removed +- [stratified keratinized epithelial stem cell](http://purl.obolibrary.org/obo/CL_1000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009371"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stratified keratinized epithelial stem cell](http://purl.obolibrary.org/obo/CL_1000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009371"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stratified squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000240` +#### Removed +- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009144"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009144"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stretch receptor cell `http://purl.obolibrary.org/obo/CL_1000082` +#### Removed +- [stretch receptor cell](http://purl.obolibrary.org/obo/CL_1000082) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009370"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stretch receptor cell](http://purl.obolibrary.org/obo/CL_1000082) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009370"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### striated muscle cell `http://purl.obolibrary.org/obo/CL_0000737` +#### Removed +- [striated muscle cell](http://purl.obolibrary.org/obo/CL_0000737) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005784"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [striated muscle cell](http://purl.obolibrary.org/obo/CL_0000737) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005784"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### stromal cell `http://purl.obolibrary.org/obo/CL_0000499` +#### Removed +- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009226"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009226"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### structural cell `http://purl.obolibrary.org/obo/CL_0000293` +#### Removed +- [structural cell](http://purl.obolibrary.org/obo/CL_0000293) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005745"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [structural cell](http://purl.obolibrary.org/obo/CL_0000293) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005745"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### subset_property `http://www.geneontology.org/formats/oboInOwl#SubsetProperty` + +#### Added +- [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) [label](http://www.w3.org/2000/01/rdf-schema#label) "subset_property"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- AnnotationProperty: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + + +### substance P secreting cell `http://purl.obolibrary.org/obo/CL_0000505` +#### Removed +- [substance P secreting cell](http://purl.obolibrary.org/obo/CL_0000505) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009230"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [substance P secreting cell](http://purl.obolibrary.org/obo/CL_0000505) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009230"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### supporting cell `http://purl.obolibrary.org/obo/CL_0000630` +#### Removed +- [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009387"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009387"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sustentacular cell `http://purl.obolibrary.org/obo/CL_0000703` +#### Removed +- [sustentacular cell](http://purl.obolibrary.org/obo/CL_0000703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009302"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sustentacular cell](http://purl.obolibrary.org/obo/CL_0000703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009302"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sympathetic cholinergic neuron `http://purl.obolibrary.org/obo/CL_3000003` +#### Removed +- [sympathetic cholinergic neuron](http://purl.obolibrary.org/obo/CL_3000003) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) + +#### Added +- [sympathetic cholinergic neuron](http://purl.obolibrary.org/obo/CL_3000003) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) + + +### sympathetic neuron `http://purl.obolibrary.org/obo/CL_0011103` +#### Removed +- [sympathetic neuron](http://purl.obolibrary.org/obo/CL_0011103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005777"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [sympathetic neuron](http://purl.obolibrary.org/obo/CL_0011103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005777"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sympathetic noradrenergic neuron `http://purl.obolibrary.org/obo/CL_3000002` +#### Removed +- [sympathetic noradrenergic neuron](http://purl.obolibrary.org/obo/CL_3000002) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) + +#### Added +- [sympathetic noradrenergic neuron](http://purl.obolibrary.org/obo/CL_3000002) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) + + +### synovial cell `http://purl.obolibrary.org/obo/CL_0000214` +#### Removed +- [synovial cell](http://purl.obolibrary.org/obo/CL_0000214) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [synovial cell](http://purl.obolibrary.org/obo/CL_0000214) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009131"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### taste receptor cell `http://purl.obolibrary.org/obo/CL_0000209` +#### Removed +- [taste receptor cell](http://purl.obolibrary.org/obo/CL_0000209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009126"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [taste receptor cell](http://purl.obolibrary.org/obo/CL_0000209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009126"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### tendon cell `http://purl.obolibrary.org/obo/CL_0000388` +#### Removed +- [tendon cell](http://purl.obolibrary.org/obo/CL_0000388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009189"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [tendon cell](http://purl.obolibrary.org/obo/CL_0000388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009189"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### terminal Schwann cell `http://purl.obolibrary.org/obo/CL_0000692` +#### Removed +- [terminal Schwann cell](http://purl.obolibrary.org/obo/CL_0000692) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009298"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [terminal Schwann cell](http://purl.obolibrary.org/obo/CL_0000692) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009298"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### testosterone secreting cell `http://purl.obolibrary.org/obo/CL_0000177` +#### Removed +- [testosterone secreting cell](http://purl.obolibrary.org/obo/CL_0000177) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009107"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [testosterone secreting cell](http://purl.obolibrary.org/obo/CL_0000177) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009107"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### tether cell `http://purl.obolibrary.org/obo/CL_0002450` +#### Removed +- [tether cell](http://purl.obolibrary.org/obo/CL_0002450) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005565"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [tether cell](http://purl.obolibrary.org/obo/CL_0002450) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005565"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### theca cell `http://purl.obolibrary.org/obo/CL_0000503` +#### Removed +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009229"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009229"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### thecogen cell `http://purl.obolibrary.org/obo/CL_0000380` +#### Removed +- [thecogen cell](http://purl.obolibrary.org/obo/CL_0000380) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005173"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [thecogen cell](http://purl.obolibrary.org/obo/CL_0000380) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005173"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### thermoreceptor cell `http://purl.obolibrary.org/obo/CL_0000205` +#### Removed +- [thermoreceptor cell](http://purl.obolibrary.org/obo/CL_0000205) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009123"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [thermoreceptor cell](http://purl.obolibrary.org/obo/CL_0000205) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009123"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### thromboblast `http://purl.obolibrary.org/obo/CL_0000828` +#### Removed +- [thromboblast](http://purl.obolibrary.org/obo/CL_0000828) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009351"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [thromboblast](http://purl.obolibrary.org/obo/CL_0000828) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009351"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### thyroid hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000452` +#### Removed +- [thyroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000452) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009210"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [thyroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000452) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009210"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### thyrotroph `http://purl.obolibrary.org/obo/CL_0000476` +#### Removed +- [thyrotroph](http://purl.obolibrary.org/obo/CL_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009218"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [thyrotroph](http://purl.obolibrary.org/obo/CL_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009218"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### tonsil germinal center B cell `http://purl.obolibrary.org/obo/CL_2000006` +#### Removed +- [tonsil germinal center B cell](http://purl.obolibrary.org/obo/CL_2000006) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [tonsil germinal center B cell](http://purl.obolibrary.org/obo/CL_2000006) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### tormogen cell `http://purl.obolibrary.org/obo/CL_0000372` +#### Removed +- [tormogen cell](http://purl.obolibrary.org/obo/CL_0000372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005171"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [tormogen cell](http://purl.obolibrary.org/obo/CL_0000372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005171"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### totipotent stem cell `http://purl.obolibrary.org/obo/CL_0000052` +#### Removed +- [totipotent stem cell](http://purl.obolibrary.org/obo/CL_0000052) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009024"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [totipotent stem cell](http://purl.obolibrary.org/obo/CL_0000052) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009024"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### tracheobronchial goblet cell `http://purl.obolibrary.org/obo/CL_0019003` +#### Removed +- [tracheobronchial goblet cell](http://purl.obolibrary.org/obo/CL_0019003) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196)) + +#### Added +- [tracheobronchial goblet cell](http://purl.obolibrary.org/obo/CL_0019003) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) + + +### transitional epithelial cell `http://purl.obolibrary.org/obo/CL_0000244` +#### Removed +- [transitional epithelial cell](http://purl.obolibrary.org/obo/CL_0000244) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009148"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [transitional epithelial cell](http://purl.obolibrary.org/obo/CL_0000244) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009148"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### transitional stage B cell `http://purl.obolibrary.org/obo/CL_0000818` +#### Removed +- [transitional stage B cell](http://purl.obolibrary.org/obo/CL_0000818) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009345"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [transitional stage B cell](http://purl.obolibrary.org/obo/CL_0000818) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009345"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### trichogen cell `http://purl.obolibrary.org/obo/CL_0000374` +#### Removed +- [trichogen cell](http://purl.obolibrary.org/obo/CL_0000374) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005169"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [trichogen cell](http://purl.obolibrary.org/obo/CL_0000374) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005169"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### type B pancreatic cell `http://purl.obolibrary.org/obo/CL_0000169` +#### Removed +- [type B pancreatic cell](http://purl.obolibrary.org/obo/CL_0000169) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009102"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [type B pancreatic cell](http://purl.obolibrary.org/obo/CL_0000169) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009102"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502` +#### Removed +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009228"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009228"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### type I pneumocyte `http://purl.obolibrary.org/obo/CL_0002062` +#### Removed +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "AT1"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ATI"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [label](http://www.w3.org/2000/01/rdf-schema#label) "type I pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 1 pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29463737"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "AT1"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29463737"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ATI"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 1 pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32491474"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type I pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary alveolar type 1 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### type II cell of adrenal medulla `http://purl.obolibrary.org/obo/CL_0002082` +#### Removed +- [type II cell of adrenal medulla](http://purl.obolibrary.org/obo/CL_0002082) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "adremergic chromaffin cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [type II cell of adrenal medulla](http://purl.obolibrary.org/obo/CL_0002082) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "adrenergic chromaffin cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### type II pneumocyte `http://purl.obolibrary.org/obo/CL_0002063` +#### Removed +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "TII"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [label](http://www.w3.org/2000/01/rdf-schema#label) "type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ATII"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8540632"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0412046911"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "AT2"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +#### Added +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary alveolar type 2 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8540632"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0412046911"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36138472"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32491474"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "AT2"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36138472"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "TII"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ATII"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + + +### umbilical artery endothelial cell `http://purl.obolibrary.org/obo/CL_2000052` +#### Removed +- [umbilical artery endothelial cell](http://purl.obolibrary.org/obo/CL_2000052) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [umbilical artery endothelial cell](http://purl.obolibrary.org/obo/CL_2000052) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### unipolar neuron `http://purl.obolibrary.org/obo/CL_0000106` +#### Removed +- [unipolar neuron](http://purl.obolibrary.org/obo/CL_0000106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009058"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [unipolar neuron](http://purl.obolibrary.org/obo/CL_0000106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009058"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### urothelial cell `http://purl.obolibrary.org/obo/CL_0000731` +#### Removed +- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009308"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009308"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### vascular associated smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000359` +#### Removed +- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009181"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009181"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### vascular lymphangioblast `http://purl.obolibrary.org/obo/CL_0005022` +#### Removed +- [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009395"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009395"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### ventricular cardiac muscle cell `http://purl.obolibrary.org/obo/CL_2000046` +#### Removed +- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +#### Added +- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + + +### vip GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023016` +#### Removed +- [vip GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + +- [vip GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + +#### Added +- [vip GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) + + +### visceral muscle cell `http://purl.obolibrary.org/obo/CL_0008007` +#### Removed +- [visceral muscle cell](http://purl.obolibrary.org/obo/CL_0008007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005070"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [visceral muscle cell](http://purl.obolibrary.org/obo/CL_0008007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005070"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### visceromotor neuron `http://purl.obolibrary.org/obo/CL_0005025` +#### Removed +- [visceromotor neuron](http://purl.obolibrary.org/obo/CL_0005025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005732"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [visceromotor neuron](http://purl.obolibrary.org/obo/CL_0005025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005732"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### visible light photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000488` +#### Removed +- [visible light photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [visible light photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009219"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### visual pigment cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0001658` +#### Removed +- [visual pigment cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0001658) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004230"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [visual pigment cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0001658) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004230"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### visual pigment cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000343` +#### Removed +- [visual pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009171"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [visual pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009171"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### xanthoblast `http://purl.obolibrary.org/obo/CL_0005002` +#### Removed +- [xanthoblast](http://purl.obolibrary.org/obo/CL_0005002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005245"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [xanthoblast](http://purl.obolibrary.org/obo/CL_0005002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005245"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### xanthophore cell `http://purl.obolibrary.org/obo/CL_0000430` +#### Removed +- [xanthophore cell](http://purl.obolibrary.org/obo/CL_0000430) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009198"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [xanthophore cell](http://purl.obolibrary.org/obo/CL_0000430) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009198"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### yolk cell `http://purl.obolibrary.org/obo/CL_0000428` +#### Removed +- [yolk cell](http://purl.obolibrary.org/obo/CL_0000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +#### Added +- [yolk cell](http://purl.obolibrary.org/obo/CL_0000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000084"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) diff --git a/src/ontology/reports/cl-edit.owl-obo-report.tsv b/src/ontology/reports/cl-edit.owl-obo-report.tsv index 33c259e99..b7bf46143 100644 --- a/src/ontology/reports/cl-edit.owl-obo-report.tsv +++ b/src/ontology/reports/cl-edit.owl-obo-report.tsv @@ -1,4 +1,6 @@ Level Rule Name Subject Property Value +WARN duplicate_scoped_synonym CL:4023064 oboInOwl:hasExactSynonym CGE interneuron +WARN duplicate_scoped_synonym CL:4023064 oboInOwl:hasRelatedSynonym CGE interneuron WARN missing_definition CL:0000028 IAO:0000115 WARN missing_definition CL:0000030 IAO:0000115 WARN missing_definition CL:0000036 IAO:0000115 @@ -26,7 +28,6 @@ WARN missing_definition CL:0000208 IAO:0000115 WARN missing_definition CL:0000217 IAO:0000115 WARN missing_definition CL:0000237 IAO:0000115 WARN missing_definition CL:0000238 IAO:0000115 -WARN missing_definition CL:0000239 IAO:0000115 WARN missing_definition CL:0000240 IAO:0000115 WARN missing_definition CL:0000241 IAO:0000115 WARN missing_definition CL:0000246 IAO:0000115 @@ -86,7 +87,6 @@ WARN missing_definition CL:0000618 IAO:0000115 WARN missing_definition CL:0000619 IAO:0000115 WARN missing_definition CL:0000661 IAO:0000115 WARN missing_definition CL:0000662 IAO:0000115 -WARN missing_definition CL:0000666 IAO:0000115 WARN missing_definition CL:0000676 IAO:0000115 WARN missing_definition CL:0000678 IAO:0000115 WARN missing_definition CL:0000684 IAO:0000115 @@ -112,8 +112,6 @@ WARN missing_definition CL:0001658 IAO:0000115 WARN missing_definition CL:0007019 IAO:0000115 WARN missing_definition CL:0010013 IAO:0000115 WARN missing_definition CL:0010014 IAO:0000115 -WARN missing_definition CL:0011025 IAO:0000115 -WARN missing_definition CL:0011028 IAO:0000115 WARN missing_definition CL:1000082 IAO:0000115 WARN missing_definition CL:1000083 IAO:0000115 WARN missing_definition CL:1000085 IAO:0000115 @@ -150,7 +148,6 @@ WARN missing_definition oboInOwl:hasRelatedSynonym IAO:0000115 WARN missing_definition oboInOwl:hasSynonymType IAO:0000115 WARN missing_definition oboInOwl:inSubset IAO:0000115 WARN missing_definition oboInOwl:shorthand IAO:0000115 -WARN missing_obsolete_label CL:0000736 rdfs:label embryonic gland hemocyte WARN missing_subset_declaration obo:cl#cellxgene_subset rdfs:subPropertyOf WARN missing_synonymtype_declaration OMO:0003000 rdfs:subPropertyOf WARN missing_synonymtype_declaration OMO:0003004 rdfs:subPropertyOf @@ -164,6 +161,7 @@ INFO missing_superclass CL:0000048 rdfs:subClassOf INFO missing_superclass CL:0000064 rdfs:subClassOf INFO missing_superclass CL:0000067 rdfs:subClassOf INFO missing_superclass CL:0000080 rdfs:subClassOf +INFO missing_superclass CL:0000082 rdfs:subClassOf INFO missing_superclass CL:0000103 rdfs:subClassOf INFO missing_superclass CL:0000104 rdfs:subClassOf INFO missing_superclass CL:0000108 rdfs:subClassOf @@ -251,12 +249,14 @@ INFO missing_superclass CL:0001082 rdfs:subClassOf INFO missing_superclass CL:0002062 rdfs:subClassOf INFO missing_superclass CL:0002067 rdfs:subClassOf INFO missing_superclass CL:0002075 rdfs:subClassOf +INFO missing_superclass CL:0002076 rdfs:subClassOf INFO missing_superclass CL:0002077 rdfs:subClassOf INFO missing_superclass CL:0002078 rdfs:subClassOf INFO missing_superclass CL:0002089 rdfs:subClassOf INFO missing_superclass CL:0002132 rdfs:subClassOf INFO missing_superclass CL:0002148 rdfs:subClassOf INFO missing_superclass CL:0002200 rdfs:subClassOf +INFO missing_superclass CL:0002202 rdfs:subClassOf INFO missing_superclass CL:0002205 rdfs:subClassOf INFO missing_superclass CL:0002206 rdfs:subClassOf INFO missing_superclass CL:0002208 rdfs:subClassOf @@ -304,7 +304,11 @@ INFO missing_superclass CL:0002569 rdfs:subClassOf INFO missing_superclass CL:0002570 rdfs:subClassOf INFO missing_superclass CL:0002608 rdfs:subClassOf INFO missing_superclass CL:0002621 rdfs:subClassOf +INFO missing_superclass CL:0002631 rdfs:subClassOf +INFO missing_superclass CL:0002632 rdfs:subClassOf +INFO missing_superclass CL:0002633 rdfs:subClassOf INFO missing_superclass CL:0002634 rdfs:subClassOf +INFO missing_superclass CL:0002652 rdfs:subClassOf INFO missing_superclass CL:0002673 rdfs:subClassOf INFO missing_superclass CL:0002681 rdfs:subClassOf INFO missing_superclass CL:0003001 rdfs:subClassOf @@ -465,7 +469,6 @@ INFO missing_superclass CL:1000378 rdfs:subClassOf INFO missing_superclass CL:1000381 rdfs:subClassOf INFO missing_superclass CL:1000382 rdfs:subClassOf INFO missing_superclass CL:1000385 rdfs:subClassOf -INFO missing_superclass CL:1000398 rdfs:subClassOf INFO missing_superclass CL:1000405 rdfs:subClassOf INFO missing_superclass CL:1000415 rdfs:subClassOf INFO missing_superclass CL:1000433 rdfs:subClassOf @@ -490,7 +493,13 @@ INFO missing_superclass CL:1000505 rdfs:subClassOf INFO missing_superclass CL:1000507 rdfs:subClassOf INFO missing_superclass CL:1000546 rdfs:subClassOf INFO missing_superclass CL:1000549 rdfs:subClassOf +INFO missing_superclass CL:1000612 rdfs:subClassOf INFO missing_superclass CL:1000692 rdfs:subClassOf +INFO missing_superclass CL:1000746 rdfs:subClassOf +INFO missing_superclass CL:1001005 rdfs:subClassOf +INFO missing_superclass CL:1001009 rdfs:subClassOf +INFO missing_superclass CL:1001099 rdfs:subClassOf +INFO missing_superclass CL:1001124 rdfs:subClassOf INFO missing_superclass CL:1001225 rdfs:subClassOf INFO missing_superclass CL:1001428 rdfs:subClassOf INFO missing_superclass CL:1001433 rdfs:subClassOf @@ -604,11 +613,8 @@ INFO missing_superclass CL:3000003 rdfs:subClassOf INFO missing_superclass CL:3000004 rdfs:subClassOf INFO missing_superclass CL:4023008 rdfs:subClassOf INFO missing_superclass CL:4023009 rdfs:subClassOf -INFO missing_superclass CL:4023011 rdfs:subClassOf INFO missing_superclass CL:4023012 rdfs:subClassOf INFO missing_superclass CL:4023013 rdfs:subClassOf -INFO missing_superclass CL:4023015 rdfs:subClassOf -INFO missing_superclass CL:4023016 rdfs:subClassOf INFO missing_superclass CL:4023017 rdfs:subClassOf INFO missing_superclass CL:4023018 rdfs:subClassOf INFO missing_superclass CL:4023019 rdfs:subClassOf @@ -623,11 +629,9 @@ INFO missing_superclass CL:4023057 rdfs:subClassOf INFO missing_superclass CL:4023058 rdfs:subClassOf INFO missing_superclass CL:4023062 rdfs:subClassOf INFO missing_superclass CL:4023063 rdfs:subClassOf -INFO missing_superclass CL:4023064 rdfs:subClassOf INFO missing_superclass CL:4023066 rdfs:subClassOf INFO missing_superclass CL:4023068 rdfs:subClassOf INFO missing_superclass CL:4023069 rdfs:subClassOf -INFO missing_superclass CL:4023070 rdfs:subClassOf INFO missing_superclass CL:4023072 rdfs:subClassOf INFO missing_superclass CL:4023074 rdfs:subClassOf INFO missing_superclass CL:4023076 rdfs:subClassOf @@ -669,6 +673,7 @@ INFO missing_superclass CL:4030017 rdfs:subClassOf INFO missing_superclass CL:4030020 rdfs:subClassOf INFO missing_superclass CL:4030021 rdfs:subClassOf INFO missing_superclass CL:4030022 rdfs:subClassOf +INFO missing_superclass CL:4030023 rdfs:subClassOf INFO missing_superclass CL:4030025 rdfs:subClassOf INFO missing_superclass CL:4030027 rdfs:subClassOf INFO missing_superclass CL:4030028 rdfs:subClassOf diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.json b/src/ontology/subsets/blood_and_immune_upper_slim.json index bb7421769..7c2d36189 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.json +++ b/src/ontology/subsets/blood_and_immune_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -661,10 +508,6 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cuboidal endothelial cell of vascular tree" - } ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -3313,32 +3156,6 @@ "val" : "2010-06-29T03:38:22Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002078", - "lbl" : "meso-epithelial cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Epithelial cell derived from mesoderm or mesenchyme.", - "xrefs" : [ "FMA:69076", "GOC:tfm" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial mesenchymal cell" - } ], - "xrefs" : [ { - "val" : "FMA:69076" - }, { - "val" : "ZFA:0009388" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-06-29T03:49:14Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002087", "lbl" : "nongranular leukocyte", @@ -3971,7 +3788,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://www.wikidata.org/entity/Q35563349" + "val" : "http://www.wikidata.org/entity/Q35563349" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-02-11T17:29:04Z" @@ -3992,62 +3809,6 @@ "val" : "2022-11-04T14:40:00Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -4055,7 +3816,7 @@ "meta" : { "definition" : { "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", - "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + "xrefs" : [ "GOC:mah", "ISBN:0815316194" ] }, "comments" : [ "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -5923,7 +5684,7 @@ "meta" : { "definition" : { "val" : "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.", - "xrefs" : [ "GOC:bf", "Wikipedia:GPCR", "http://www.iuphar-db.org" ] + "xrefs" : [ "GOC:bf", "Wikipedia:GPCR" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { @@ -6795,7 +6556,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", + "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", "xrefs" : [ "GOC:mah", "ISBN:0716731363", "PMID:22323285" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -8936,7 +8697,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -8966,7 +8727,7 @@ "meta" : { "definition" : { "val" : "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:18391171" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", @@ -8988,7 +8749,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -10838,7 +10599,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -11250,13 +11011,16 @@ "meta" : { "definition" : { "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", - "xrefs" : [ "GOC:go_curators", "http://www.metacyc.org" ] + "xrefs" : [ "GOC:go_curators" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "primary metabolism" } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" @@ -13182,40 +12946,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071704", - "lbl" : "organic substance metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance metabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-03-08T03:32:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0071707", "lbl" : "immunoglobulin heavy chain V-D-J recombination", @@ -14181,62 +13911,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1902105", "lbl" : "regulation of leukocyte differentiation", @@ -14502,260 +14176,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], - "xrefs" : [ { - "val" : "IAO:0000233" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." - }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -15424,73 +14844,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -19427,6 +18780,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -19539,2856 +18916,6805 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" - }, - "xrefs" : [ { - "val" : "RO:0000056" + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "val" : "protein" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" - }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], + "xrefs" : [ { + "val" : "galen:Tube" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000055", + "lbl" : "vessel", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "A tubular structure that contains, conveys body fluid, such as blood or lymph.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000060", + "lbl" : "anatomical wall", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.", + "xrefs" : [ "FMA:82482" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "wall" + }, { + "pred" : "hasExactSynonym", + "val" : "wall of organ", + "xrefs" : [ "FMA:82482" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ wall", + "xrefs" : [ "FMA:82482" ] + } ], + "xrefs" : [ { + "val" : "FMA:82482" + }, { + "val" : "galen:Wall" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0009915" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001025", - "lbl" : "located in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000061", + "lbl" : "anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "CARO:0000003" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological structure" + }, { + "pred" : "hasExactSynonym", + "val" : "connected biological structure", + "xrefs" : [ "CARO:0000003" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010825" + }, { + "val" : "AEO:0000003" + }, { + "val" : "BILA:0000003" + }, { + "val" : "CARO:0000003" + }, { + "val" : "EHDAA2:0003003" + }, { + "val" : "EMAPA:0" + }, { + "val" : "FBbt:00007001" + }, { + "val" : "FMA:305751" + }, { + "val" : "FMA:67135" + }, { + "val" : "GAID:781" + }, { + "val" : "HAO:0000003" + }, { + "val" : "MA:0003000" + }, { + "val" : "MESH:D000825" + }, { + "val" : "SCTID:362889002" + }, { + "val" : "TAO:0000037" + }, { + "val" : "TGMA:0001823" + }, { + "val" : "VHOG:0001759" + }, { + "val" : "XAO:0003000" + }, { + "val" : "ZFA:0000037" + }, { + "val" : "http://dbpedia.org/ontology/AnatomicalStructure" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Located_in" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", - "lbl" : "2D boundary of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000062", + "lbl" : "organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + "val" : "Anatomical structure that performs a specific function or group of functions [WP].", + "xrefs" : [ "Wikipedia:Organ_(anatomy)" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "anatomical unit" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body organ" + }, { + "pred" : "hasRelatedSynonym", + "val" : "element", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:4" + }, { + "val" : "CARO:0020004" + }, { + "val" : "EFO:0000634" + }, { + "val" : "EMAPA:35949" + }, { + "val" : "ENVO:01000162" + }, { + "val" : "FMA:67498" + }, { + "val" : "MA:0003001" + }, { + "val" : "NCIT:C13018" + }, { + "val" : "SCTID:272625005" + }, { + "val" : "UMLS:C0178784" + }, { + "val" : "WBbt:0003760" + }, { + "val" : "Wikipedia:Organ_(anatomy)" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", - 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Cleavage ends with the formation of the blastula.", + "xrefs" : [ "GO:0040016", "Wikipedia:Cleavage_(embryo)" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000107" + }, { + "val" : "BilaDO:0000006" + }, { + "val" : "EFO:0001290" + }, { + "val" : "FBdv:00000054" + }, { + "val" : "MESH:D002970" + }, { + "val" : "MmusDv:0000004" + }, { + "val" : "OGES:000015" + }, { + "val" : "OGES:000020" + }, { + "val" : "PdumDv:0000200" + }, { + "val" : "Wikipedia:Cleavage_(embryo)" + }, { + "val" : "XAO:1000004" + }, { + "val" : "ZFS:0000046" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some Y?)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", - "lbl" : "overlaps", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000108", + "lbl" : "blastula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" + "val" : "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "xrefs" : [ { - "val" : "RO:0002131" + "val" : "BILS:0000108" + }, { + "val" : "BilaDO:0000007" + }, { + "val" : "EFO:0001282" + }, { + "val" : "HsapDv:0000006" + }, { + "val" : "MmusDv:0000007" + }, { + "val" : "OGES:000003" + }, { + "val" : "OGES:000016" + }, { + "val" : "OGES:000021" + }, { + "val" : "WBls:0000005" + }, { + "val" : "Wikipedia:Blastula" + }, { + "val" : "XAO:1000003" + }, { + "val" : "ZFS:0000045" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adding a preceding stage 'morula stage' as part of cleavage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002132", - "lbl" : "has fasciculating neuron projection", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002134", - "lbl" : "innervates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000109", + "lbl" : "gastrula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that ( some ( that some Y?)))" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002150", - "lbl" : "continuous with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + "val" : "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.", + "xrefs" : [ "GO:0007369" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blastocystis trilaminaris stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000109" + }, { + "val" : "BilaDO:0000008" + }, { + "val" : "EFO:0001296" + }, { + "val" : "FBdv:00005317" + }, { + "val" : "HsapDv:0000010" + }, { + "val" : "MmusDv:0000013" + }, { + "val" : "OGES:000004" + }, { + "val" : "OGES:000019" + }, { + "val" : "WBls:0000010" + }, { + "val" : "XAO:1000005" + }, { + "val" : "ZFS:0000047" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", - "lbl" : "shares ancestor with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." - }, - "comments" : [ "VBO calls this homologous_to" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", - "lbl" : "only in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000110", + "lbl" : "neurula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." + "val" : "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. 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Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." - }, + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." - }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "val" : "BilaDO:0000010" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" - }, + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. 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When one structure connects two others it unites some aspect of the function or role they play within the system." + "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "xrefs" : [ "Wikipedia:Mouth", "https://github.com/obophenotype/uberon/wiki/The-digestive-tract" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio oralis", + "xrefs" : [ "BTO:0004698", "FMA:49184", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "cavital oralis", + "xrefs" : [ "Wikipedia:Mouth" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavitas oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavum oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth cavity", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral region", + "xrefs" : [ "EHDAA2:0001326" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral vestibule", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "rima oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "stoma" + }, { + "pred" : "hasRelatedSynonym", + "val" : "stomatodaeum", + "xrefs" : [ "VHOG:0000812" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trophic apparatus", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibule of mouth", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibulum oris", + "xrefs" : [ "BTO:0001090" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010355" + }, { + "val" : "BTO:0001090" + }, { + "val" : "BTO:0004698" + }, { + "val" : "CALOHA:TS-1315" + }, { + "val" : "EFO:0000825" + }, { + "val" : "EHDAA2:0001326" + }, { + "val" : "EHDAA:542" + }, { + "val" : "EMAPA:16262" + }, { + "val" : "FBbt:00003126" + }, { + "val" : "FMA:49184" + }, { + "val" : "GAID:75" + }, { + "val" : "MA:0000341" + }, { + "val" : "MA:0002474" + }, { + "val" : "MAT:0000038" + }, { + "val" : "MESH:D009055" + }, { + "val" : "MIAA:0000038" + }, { + "val" : "SCTID:21082005" + }, { + "val" : "TADS:0000040" + }, { + "val" : "TAO:0000547" + }, { + "val" : "TAO:0000590" + }, { + "val" : "TGMA:0000131" + }, { + "val" : "VHOG:0000280" + }, { + "val" : "VHOG:0000812" + }, { + "val" : "Wikipedia:Mouth" + }, { + "val" : "XAO:0003029" + }, { + "val" : "ZFA:0000547" + }, { + "val" : "ZFA:0000590" + }, { + "val" : "galen:Mouth" + }, { + "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" + } ], "basicPropertyValues" : [ { - 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"val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + "val" : "A fluid that is composed of blood plasma and erythrocytes.", + "xrefs" : [ "FMA:9670", "Wikipedia:Blood", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/9" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of blood" + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate blood" + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole blood", + "xrefs" : [ "BTO:0000089" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000046" + }, { + "val" : "BTO:0000089" + }, { + "val" : "CALOHA:TS-0079" + }, { + "val" : "EFO:0000296" + }, { + "val" : "EHDAA2:0000176" + }, { + "val" : "EHDAA:418" + }, { + "val" : "EMAPA:16332" + }, { + "val" : "ENVO:02000027" + }, { + "val" : "EV:0100047" + }, { + "val" : "FMA:9670" + }, { + "val" : "GAID:965" + }, { + "val" : "MA:0000059" + }, { + "val" : "MESH:D001769" + }, { + "val" : "MIAA:0000315" + }, { + "val" : "NCIT:C12434" + }, { + "val" : "TAO:0000007" + }, { + "val" : "UMLS:C0005767" + }, { + "val" : "VHOG:0000224" + }, { + "val" : "Wikipedia:Blood" + }, { + "val" : "XAO:0000124" + }, { + "val" : "ZFA:0000007" + }, { + "val" : "galen:Blood" + } ], "basicPropertyValues" : [ { - 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For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000179", + "lbl" : "haemolymphatic fluid", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + "val" : "Circulating fluid that is part of the hemolymphoid system. 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For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-04-08T04:38:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", + "lbl" : "blastula", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. 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The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blastula embryo", + "xrefs" : [ "BILA:0000059" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastosphere", + "xrefs" : [ "Wikipedia:Blastula" ] + } ], "xrefs" : [ { - "val" : "RO:0002180" + "val" : "BILA:0000059" + }, { + "val" : "BTO:0000128" + }, { + "val" : "GAID:1294" + }, { + "val" : "MESH:D036703" + }, { + "val" : "OGEM:000006" + }, { + "val" : "Wikipedia:Blastula" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007011" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - 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body continues after death stage" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002225", - "lbl" : "develops from part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002226", - "lbl" : "develops in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops_in y if x is located in y whilst x is developing" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", - "lbl" : "ends", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000475", + "lbl" : "organism subdivision", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of ends with" + "val" : "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.", + "xrefs" : [ "CARO:0000032", "CARO:DOS", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomic region", + "xrefs" : [ "MA:0002433" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "body part" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body region", + "xrefs" : [ "FMA:7153" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardinal body part", + "xrefs" : [ "FMA:7153" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010053" + }, { + "val" : "AEO:0000032" + }, { + "val" : "BILA:0000032" + }, { + "val" : "BIRNLEX:7" + }, { + "val" : "CALOHA:TS-2084" + }, { + "val" : "CARO:0000032" + }, { + "val" : "EFO:0000808" + }, { + "val" : "EHDAA2:0003032" + }, { + "val" : "EMAPA:36031" + }, { + "val" : "FBbt:00007009" + }, { + "val" : "FMA:7153" + }, { + "val" : "HAO:0000032" + }, { + "val" : "MA:0002433" + }, { + "val" : "MAT:0000293" + }, { + "val" : "MESH:D001829" + }, { + "val" : "MIAA:0000293" + }, { + "val" : "NCIT:C32221" + }, { + "val" : "TAO:0001308" + }, { + "val" : "TGMA:0001840" + }, { + "val" : "UMLS:C0229962" + }, { + "val" : "VHOG:0001758" + }, { + "val" : "Wikipedia:Body_part" + }, { + "val" : "XAO:0003013" + }, { + "val" : "ZFA:0001308" + }, { + "val" : "galen:BodyPart" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", - "lbl" : "ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000476", + "lbl" : "acellular anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "acellular anatomical structures", + "xrefs" : [ "ZFA:0000382" ] + } ], "xrefs" : [ { - "val" : "RO:0002230" + "val" : "AAO:0010268" + }, { + "val" : "AEO:0000040" + }, { + "val" : "BILA:0000040" + }, { + "val" : "CARO:0000040" + }, { + "val" : "EHDAA2:0003040" + }, { + "val" : "FBbt:00007013" + }, { + "val" : "FMA:63863" + }, { + "val" : "HAO:0000040" + }, { + "val" : "TAO:0000382" + }, { + "val" : "TGMA:0001841" + }, { + "val" : "XAO:0003162" + }, { + "val" : "ZFA:0000382" } ], "basicPropertyValues" : [ { - 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"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002231" + "val" : "FBbt:00007277" + }, { + "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_start_location" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002232", - "lbl" : "has end location", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", + "lbl" : "tissue", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", + "xrefs" : [ "CARO:0000043" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of tissue", + "xrefs" : [ "CARO:0000043" ] + }, { + "pred" : "hasExactSynonym", + "val" : "tissue portion" + }, { + "pred" : "hasNarrowSynonym", + "val" : "simple tissue", + "xrefs" : [ "AEO:0000043" ] + } ], "xrefs" : [ { - "val" : "RO:0002232" + "val" : "AAO:0000607" + }, { + "val" : "AAO:0010054" + }, { + "val" : "AEO:0000043" + }, { + "val" : "BILA:0000043" + }, { + "val" : "BIRNLEX:19" + }, { + "val" : "CALOHA:TS-2090" + }, { + "val" : "CARO:0000043" + }, { + "val" : "EHDAA2:0003043" + }, { + "val" : "EMAPA:35868" + }, { + "val" : "FBbt:00007003" + }, { + "val" : "FMA:9637" + }, { + "val" : "HAO:0000043" + }, { + "val" : "MA:0003002" + }, { + "val" : "MESH:D014024" + }, { + "val" : "NCIT:C12801" + }, { + "val" : "TAO:0001477" + }, { + "val" : "TGMA:0001844" + }, { + "val" : "UMLS:C0040300" + }, { + "val" : "VHOG:0001757" + }, { + "val" : "WBbt:0005729" + }, { + "val" : "XAO:0003040" + }, { + "val" : "ZFA:0001477" + }, { + "val" : "galen:Tissue" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "changed label and definition to reflect CARO2" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_end_location" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", - "lbl" : "has input", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000481", + "lbl" : "multi-tissue structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + "val" : "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.", + "xrefs" : [ "CARO:0000055", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "multi-tissue structures", + "xrefs" : [ "ZFA:0001488" ] + } ], "xrefs" : [ { - "val" : "RO:0002233" + "val" : "AAO:0010048" + }, { + "val" : "AEO:0000055" + }, { + "val" : "BILA:0000055" + }, { + "val" : "CARO:0000055" + }, { + "val" : "EHDAA2:0003055" + }, { + "val" : "FBbt:00007010" + }, { + "val" : "HAO:0000055" + }, { + "val" : "TAO:0001488" + }, { + "val" : "TGMA:0001847" + }, { + "val" : "VHOG:0001762" + }, { + "val" : "XAO:0003037" + }, { + "val" : "ZFA:0001488" } ], "basicPropertyValues" : [ { - 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"plasma", + "xrefs" : [ "MA:0002501" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "portion of plasma", + "xrefs" : [ "FMA:62970" ] + }, { + "pred" : "hasExactSynonym", + "val" : "blood plasm" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of blood plasma" + } ], + "xrefs" : [ { + "val" : "BTO:0000131" + }, { + "val" : "CALOHA:TS-0800" + }, { + "val" : "EFO:0001905" + }, { + "val" : "EMAPA:35690" + }, { + "val" : "FMA:62970" + }, { + "val" : "GAID:1178" + }, { + "val" : "MA:0002501" + }, { + "val" : "MAT:0000052" + }, { + "val" : "MESH:D010949" + }, { + "val" : "MIAA:0000052" + }, { + "val" : "NCIT:C13356" + }, { + "val" : "UMLS:C0032105" + }, { + "val" : "Wikipedia:Blood_plasma" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "lbl" : "blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vessel through which blood circulates in the body.", + "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "vascular element", + "xrefs" : [ "EMAPA:35993" ] + }, { + "pred" : "hasExactSynonym", + "val" : "region of vascular tree organ", + "xrefs" : [ "FMA:50722" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vascular tree organ region", + "xrefs" : [ "FMA:50722" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "vas sanguineum", + "xrefs" : [ "Wikipedia:Blood_vessel" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011004" + }, { + "val" : 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Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].", + "xrefs" : [ "FMA:63916", "MESH:A10.272.491", "https://github.com/obophenotype/uberon/issues/225" ] + }, + "comments" : [ "The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "BTO:0000393" + }, { + "val" : "CALOHA:TS-0278" + }, { + "val" : "EFO:0002548" + }, { + "val" : "FMA:63916" + }, { + "val" : "GAID:520" + }, { + "val" : "MESH:D004727" + }, { + "val" : "NCIT:C12481" + }, { + "val" : "SCTID:27168002" + }, { + "val" : "UMLS:C0014257" + }, { + "val" : "galen:Endothelium" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002049", + "lbl" : "vasculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.", + "xrefs" : [ "ZFA:0005249" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "vascular network", + "xrefs" : [ "FMA:69050" ] + } ], + "xrefs" : [ { + "val" : "BTO:0003718" + }, { + "val" : "FMA:69050" + }, { + "val" : "TAO:0005249" + }, { + "val" : "ZFA:0005249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "see also: vascular system. Consider merging?" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002050", + "lbl" : "embryonic structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical structure that is part of an embryo.", + "xrefs" : [ "BTO:0000174", "ZFIN:curator" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "developing embryonic structure", + "xrefs" : [ "FBbt:00004208" ] + }, { + "pred" : "hasExactSynonym", + "val" : "embryonic anatomical structure", + "xrefs" : [ "RETIRED_EHDAA2:0003169" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "developing structure" + }, { + "pred" : "hasRelatedSynonym", + "val" : "embryonale Struktur", + "xrefs" : [ "BTO:0000174" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "embryonic structures", + "xrefs" : [ "ZFA:0001105" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000138" + }, { + "val" : "BILA:0000034" + }, { + "val" : "BTO:0000174" + }, { + "val" : "CALOHA:TS-2110" + }, { + "val" : "EFO:0000461" + }, { + "val" : "FBbt:00004208" + }, { + "val" : "FMA:69067" + }, { + "val" : "GAID:407" + }, { + "val" : "MESH:D004628" + }, { + "val" : "NCIT:C13229" + }, { + "val" : "RETIRED_EHDAA2:0003169" + }, { + "val" : "SCTID:667009" + }, { + "val" : "TAO:0001105" + }, { + "val" : "UMLS:C0013948" + }, { + "val" : "VSAO:0000178" + }, { + "val" : "XAO:0003042" + }, { + "val" : "ZFA:0001105" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002075", + "lbl" : "viscus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.", + "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "visceral organ", + "xrefs" : [ "RETIRED_EHDAA2:0002201" ] + }, { + "pred" : "hasExactSynonym", + "val" : "visceral organ system", + "xrefs" : [ "MA:0000019" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "splanchnic tissue", + "xrefs" : [ "BTO:0001491" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "viscera" + }, { + "pred" : "hasRelatedSynonym", + "val" : "visceral tissue", + "xrefs" : [ "BTO:0001491" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010386" + }, { + "val" : "BTO:0001491" + }, { + "val" : "EHDAA:512" + }, { + "val" : "EMAPA:16245" + }, { + "val" : "FMA:7085" + }, { + "val" : "MA:0000019" + }, { + "val" : "MESH:D014781" + }, { + "val" : "NCIT:C28287" + }, { + "val" : "RETIRED_EHDAA2:0002201" + }, { + "val" : "SCTID:118760003" + }, { + "val" : "UMLS:C0042779" + }, { + "val" : "Wikipedia:Viscus" + }, { + "val" : "XAO:0003034" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", + "lbl" : "postcranial axial skeleton", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", + "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] + }, + "comments" : [ "previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "axial skeleton", + "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] + }, { + "pred" : "hasExactSynonym", + "val" : "post-cranial axial skeleton" + } ], + "xrefs" : [ { + "val" : "AAO:0000034" + }, { + "val" : "EFO:0000942" + }, { + "val" : "EHDAA2:0000161" + }, { + "val" : "EHDAA:5049" + }, { + "val" : "EMAPA:37721" + }, { + "val" : "FMA:71221" + }, { + "val" : "MA:0002986" + }, { + "val" : "MAT:0000148" + }, { + "val" : "MIAA:0000148" + }, { + "val" : "TAO:0000317" + }, { + "val" : "VHOG:0000317" + }, { + "val" : "VSAO:0000093" + }, { + "val" : "XAO:0003073" + }, { + "val" : "ZFA:0000317" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", + "lbl" : "trunk", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.", + "xrefs" : [ "TAO:0001115", "UBERONREF:0000006", "Wikipedia:Torso" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "thoracolumbar region" + }, { + "pred" : "hasExactSynonym", + "val" : "torso" + }, { + "pred" : "hasExactSynonym", + "val" : "trunk region", + "xrefs" : [ "XAO:0000054" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Rumpf", + "xrefs" : [ "BTO:0001493" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010339" + }, { + "val" : "BILA:0000116" + }, { + "val" : "BTO:0001493" + }, { + "val" : "CALOHA:TS-1071" + }, { + "val" : "EFO:0000966" + }, { + "val" : "EMAPA:31857" + }, { + "val" : "FMA:7181" + }, { + "val" : "MA:0000004" + }, { + "val" : "MAT:0000296" + }, { + "val" : 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From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].", + "xrefs" : [ "Wikipedia:Sclerotome", "XB:curator", "https://github.com/obophenotype/uberon/issues/316" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "sclerotomes", + "xrefs" : [ "TAO:0001080" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "sclerotomus", + "xrefs" : [ "Wikipedia:Sclerotome" ] + } ], "xrefs" : [ { - "val" : "RO:0002427" + "val" : "AAO:0010571" + }, { + "val" : "AEO:0000212" + }, { + "val" : "EHDAA2:0003439" + }, { + "val" : "EMAPA:31159" + }, { + "val" : "FMA:295652" + }, { + "val" : "NCIT:C34287" + }, { + "val" : "TAO:0001080" + }, { + "val" : "UMLS:C0183176" + }, { + "val" : "VHOG:0000680" + }, { + "val" : "Wikipedia:Sclerotome" + }, { + "val" : "XAO:0000397" + }, { + "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_downstream_of_or_within" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", - "lbl" : "involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", - "lbl" : "involved in or involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", - "lbl" : "contributes to morphology of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. 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Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", - "lbl" : "composed primarily of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", - "lbl" : "has part that occurs in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", + "lbl" : "compound organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", + "xrefs" : [ "CARO:0000024" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "lbl" : "receives input from", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "lbl" : "sends output to", - "type" : "PROPERTY", - "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "organ" + } ], + "xrefs" : [ { + "val" : "AAO:0010015" + }, { + "val" : "AEO:0000024" + }, { + "val" : "BILA:0000024" + }, { + "val" : "CARO:0000024" + }, { + "val" : "EHDAA2:0003024" + }, { + "val" : "HAO:0000024" + }, { + "val" : "TADS:0000598" + }, { + "val" : "TAO:0000496" + }, { + "val" : "TGMA:0001837" + }, { + "val" : "VHOG:0001723" + }, { + "val" : "XAO:0003041" + }, { + "val" : "ZFA:0000496" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", - "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", - "lbl" : "existence starts during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002489", - "lbl" : "existence starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002490", - "lbl" : "existence overlaps", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002491", - "lbl" : "existence starts and ends during", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", + "lbl" : "mesenchyme", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.", + "xrefs" : [ "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up", "https://en.wikipedia.org/wiki/Mesenchyme", "https://github.com/obophenotype/uberon/issues/1641" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "exists during" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", - "lbl" : "existence ends during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002493", - "lbl" : "existence ends with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", - "lbl" : "transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002495", - "lbl" : "immediate transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002496", - "lbl" : "existence starts during or after", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", - "lbl" : "existence ends during or before", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002500", - "lbl" : "causal agent in process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002501", - "lbl" : "causal relation between processes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002502", - "lbl" : "depends on", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/BFO_0000169" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002551", - "lbl" : "has skeleton", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002565", - "lbl" : "results in movement of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "val" : "mesenchymal tissue" + }, { + "pred" : "hasExactSynonym", + "val" : "mesenchyme tissue" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of mesenchymal tissue" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of mesenchyme tissue" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "mesenchyma", + "xrefs" : [ "Wikipedia:Mesenchyme" ] + } ], "xrefs" : [ { - "val" : "RO:0002565" + "val" : "AAO:0010427" + }, { + "val" : "AEO:0000145" + }, { + "val" : "BTO:0001393" + }, { + "val" : "CALOHA:TS-0620" + }, { + "val" : "EHDAA2:0003145" + }, { + "val" : "EV:0100007" + }, { + "val" : "NCIT:C13301" + }, { + "val" : "TAO:0000393" + }, { + "val" : "UMLS:C0162415" + }, { + "val" : "VHOG:0000170" + }, { + "val" : "Wikipedia:Mesenchyme" + }, { + "val" : "XAO:0003046" + }, { + "val" : "ZFA:0000393" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_movement_of" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002567", - "lbl" : "biomechanically related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002568", - "lbl" : "has muscle antagonist", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002569", - "lbl" : "has branching part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of branching part of" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002570", - "lbl" : "conduit for", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", + "lbl" : "future coelemic cavity lumen", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "future coelomic cavity lumen" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body cavity precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002571", - "lbl" : "lumen of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", + "lbl" : "intraembryonic coelom", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", + "xrefs" : [ "MGI:anna", "MP:0012187" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "somatic coelom", + "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] + } ], + "xrefs" : [ { + "val" : "EHDAA:251" + }, { + "val" : "EMAPA:16088" + }, { + "val" : "NCIT:C34195" + }, { + "val" : "UMLS:C1512940" + }, { + "val" : "VHOG:0000316" + }, { + "val" : "Wikipedia:Intraembryonic_coelom" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002572", - "lbl" : "luminal space of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", + "lbl" : "epithelial tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", + "xrefs" : [ "GO:0060562", "PMID:12526790" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "epithelial or endothelial tube" + } ], + "xrefs" : [ { + "val" : "AEO:0000114" + }, { + "val" : "EHDAA2:0003114" + }, { + "val" : "FBbt:00007474" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - 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} - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002588", - "lbl" : "results in assembly of", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "foramen", + "xrefs" : [ "EHDAA2:0003080" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasNarrowSynonym", + "val" : "foramina", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "opening" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "ostia" + }, { + "pred" : "hasRelatedSynonym", + "val" : "ostium" + } ], "xrefs" : [ { - "val" : "RO:0002588" + "val" : "AEO:0000080" + }, { + "val" : "EHDAA2:0003080" + }, { + "val" : "FMA:242873" + }, { + "val" : "SCTID:346902003" + }, { + "val" : "Wikipedia:Foramen" } ], "basicPropertyValues" : [ { - 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Editors notes: TODO - develops_from" ], "xrefs" : [ { - "val" : "RO:0012003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "val" : "EMAPA:37744" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-06-08T17:21:33Z" + "val" : "MA:0003047" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "SCTID:309311006" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "acts_on_population_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012004", - "lbl" : "is small molecule regulator of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "val" : "VSAO:0000015" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-06-24T13:15:17Z" + "val" : "XAO:0004038" + }, { + "val" : "ZFA:0005619" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012005", - "lbl" : "is small molecule activator of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", + "lbl" : "skeletal element", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" + "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "AAO:0011129" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-06-24T13:15:26Z" + "val" : "TAO:0001890" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012008", - "lbl" : "results in fusion of", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0012008" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "val" : "VSAO:0000128" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-02-26T07:28:29Z" + "val" : "XAO:0004012" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "ZFA:0005494" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fusion_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013001", - "lbl" : "has synaptic IO in region", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "has synaptic input or output in" + "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:26:52Z" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013007", - "lbl" : "has sensory dendrite in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", + "lbl" : "articular system", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." + "val" : "Anatomical system that consists of all the joints of the body.", + "xrefs" : [ "VSAO:0000181" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has sensory dendrite location" + "val" : "joint system", + "xrefs" : [ "FMA:23878" ] }, { "pred" : "hasExactSynonym", - "val" : "has sensory terminal in" + "val" : "set of all joints of body", + "xrefs" : [ "FMA:23878" ] }, { - "pred" : "hasExactSynonym", - "val" : "has sensory terminal location" + "pred" : "hasRelatedSynonym", + "val" : "set of all joints" + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of joints of body", + "xrefs" : [ "FMA:23878" ] } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" + "xrefs" : [ { + "val" : "EMAPA:35150" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-20T12:10:09Z" + "val" : "FMA:23878" + }, { + "val" : "MA:0003007" + }, { + "val" : "SCTID:361827000" + }, { + "val" : "VSAO:0000181" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015006", - "lbl" : "different in magnitude relative to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). 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Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015010", - "lbl" : "has relative magnitude", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015011", - "lbl" : "has cross section", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", + "lbl" : "cardiovascular system endothelium", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "val" : "An endothelium that is part of the cardiovascular system.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - 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Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blastula embryo", - "xrefs" : [ "BILA:0000059" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastosphere", - "xrefs" : [ "Wikipedia:Blastula" ] - } ], + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "BILA:0000059" + "val" : "BILA:0000010" }, { - "val" : "BTO:0000128" + "val" : "CARO:0001002" }, { - "val" : "GAID:1294" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "MESH:D036703" + "val" : "FMA:24137" }, { - "val" : "OGEM:000006" + "val" : "NCIT:C34022" }, { - "val" : "Wikipedia:Blastula" + "val" : "UMLS:C1515977" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check relationship with epiblast. 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See https://github.com/obophenotype/uberon/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "val" : "consider FBbt:00005541 ! cardiogenic mesoderm" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "review EHDAA2 placement" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", + "lbl" : "cleaving embryo", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Organism at the cleavage stage.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "BILA:0000058" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", + "lbl" : "presumptive gut", + "type" : "CLASS", + "meta" : { "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "body fluid or substance", - "xrefs" : [ "MA:0002450" ] - }, { - "pred" : "hasExactSynonym", - "val" : "body substance", - "xrefs" : [ "FMA:9669" ] + "val" : "future digestive tract" }, { "pred" : "hasExactSynonym", - "val" : "organism substance", - "xrefs" : [ "CARO:0000004" ] + "val" : "future digestive tube" }, { "pred" : "hasExactSynonym", - 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In vertebrates, this is based on the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "simple epithelium", - "xrefs" : [ "FMA:45561" ] + "val" : "axial subdivision of organism" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "unilaminar epithelia", - "xrefs" : [ "ZFA:0001495" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010062" - }, { - "val" : "AEO:0000073" - }, { - "val" : "BILA:0000073" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000073" - }, { - "val" : "EHDAA2:0003073" - }, { - "val" : "FMA:45561" - }, { - "val" : "HAO:0000073" - }, { - "val" : "NCIT:C33554" - }, { - "val" : "SCTID:309043004" - }, { - "val" : "TAO:0001495" - }, { - "val" : "UMLS:C0682574" - }, { - "val" : "XAO:0004007" + "val" : "body segment" }, { - "val" : "ZFA:0001495" + "pred" : "hasRelatedSynonym", + "val" : "main body segment" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" + "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000915", - "lbl" : "thoracic segment of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", + "lbl" : "embryonic cardiovascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Subdivision of trunk that lies between the head and the abdomen.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A cardiovascular system that is part of a conceptus.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "thorax", - "xrefs" : [ "MA:0000022" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "anterior subdivision of trunk" + "val" : "conceptus cardiovascular system" }, { "pred" : "hasRelatedSynonym", - "val" : "upper body" + "val" : "embryonic circulatory system" }, { "pred" : "hasRelatedSynonym", - "val" : "upper trunk", - "xrefs" : [ "FMA:259209" ] + "val" : "fetal circulatory system" } ], "xrefs" : [ { - "val" : "EMAPA:35862" - }, { - "val" : "FMA:259209" - }, { - "val" : "MA:0000022" + "val" : "EHDAA2:0000216" }, { - "val" : "SCTID:302551006" + "val" : "FMA:305965" }, { - "val" : "Wikipedia:Thorax" + "val" : "NCIT:C34148" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24613,155 +27467,110 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000922", - "lbl" : "embryo", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", + "lbl" : "coelom", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", - "xrefs" : [ "BTO:0000379", "FB:FBrf0039741", "FB:FBrf0041814", "GO:0009790", "Wikipedia:Embryo" ] + "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic organism", - "xrefs" : [ "BILA:0000056" ] + "pred" : "hasNarrowSynonym", + "val" : "enterocoelom", + "xrefs" : [ "NCBITaxon:33511" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "haemocoelom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "schizocoelom" }, { "pred" : "hasRelatedSynonym", - "val" : "developing organism", - "xrefs" : [ "BILA:0000056" ] + "val" : "coelem" }, { "pred" : "hasRelatedSynonym", - "val" : "developmental tissue" + "val" : "coelomic cavity", + "xrefs" : [ "EHDAA2:0004731" ] } ], "xrefs" : [ { - "val" : "AAO:0011035" - }, { - "val" : "AEO:0000169" - }, { - "val" : "BILA:0000056" - }, { - "val" : "BSA:0000039" - }, { - "val" : "BTO:0000379" - }, { - "val" : "CALOHA:TS-0229" - }, { - "val" : "EFO:0001367" - }, { - "val" : "EHDAA2:0000002" - }, { - "val" : "EHDAA2_RETIRED:0003236" - }, { - "val" : "EHDAA:38" - }, { - "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" - }, { - "val" : "FMA:69068" - }, { - "val" : "GAID:963" - }, { - "val" : "MAT:0000226" - }, { - "val" : "MESH:D004622" - }, { - "val" : "MIAA:0000019" - }, { - "val" : "NCIT:C28147" - }, { - "val" : "OGEM:000001" - }, { - "val" : "SCTID:57991002" - }, { - "val" : "UMLS:C0013935" - }, { - "val" : "VHOG:0001766" + "val" : "EHDAA2:0004731" }, { - "val" : "Wikipedia:Embryo" + "val" : "Wikipedia:Coelom" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." }, { - "val" : "XAO:0000113" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { - "val" : "ZFA:0000103" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", + "lbl" : "meso-epithelium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesoderm-derived epithelium" }, { - "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" + "pred" : "hasExactSynonym", + "val" : "mesoepithelium" + } ], + "xrefs" : [ { + "val" : "FMA:86452" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/503" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "lbl" : "germ layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012429", + "lbl" : "hematopoietic tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.", - "xrefs" : [ "Wikipedia:Germ_layer", "https://github.com/obophenotype/uberon/issues/203" ] + "val" : "Blood-forming tissue, consisting of reticular fibers and cells.", + "xrefs" : [ "http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue" ] }, - "comments" : [ "Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "embryonic tissue", - "xrefs" : [ "FMA:69069" ] + "pred" : "hasExactSynonym", + "val" : "haemopoietic tissue", + "xrefs" : [ "FMA:14073" ] }, { "pred" : "hasExactSynonym", - "val" : "germinal layer", - "xrefs" : [ "ncithesaurus:Germinal_Layer" ] + "val" : "hematopoietic tissue", + "xrefs" : [ "FMA:14073" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "primary germ layer", - "xrefs" : [ "GO:0001704", "ZFA:0001122" ] + "pred" : "hasExactSynonym", + "val" : "hemopoietic tissue", + "xrefs" : [ "FMA:14073" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layer" + "pred" : "hasExactSynonym", + "val" : "textus haemopoieticus", + "xrefs" : [ "FMA:14073" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layers" + "pred" : "hasNarrowSynonym", + "val" : "bone marrow tissue", + "xrefs" : [ "NCBITaxon:9606" ] } ], "xrefs" : [ { - "val" : "AAO:0000480" - }, { - "val" : "BILA:0000035" - }, { - "val" : "BTO:0000556" - }, { - "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" - }, { - "val" : "FMA:69069" - }, { - "val" : "GAID:1303" - }, { - "val" : "MESH:D005855" - }, { - "val" : "NCIT:C12950" - }, { - "val" : "NCIT:C54105" - }, { - "val" : "TAO:0001122" - }, { - "val" : "UMLS:C0920502" - }, { - "val" : "UMLS:C1708239" - }, { - "val" : "VHOG:0001223" + "val" : "CALOHA:TS-2142" }, { - "val" : "Wikipedia:Germ_layer" + "val" : "FMA:14073" }, { - "val" : "XAO:0003011" + "val" : "NCIT:C13051" }, { - "val" : "ZFA:0001122" + "val" : "UMLS:C0229619" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24769,483 +27578,250 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", - "lbl" : "ectoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", + "lbl" : "subdivision of tube", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013686", + "lbl" : "anatomical conduit space", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", - "xrefs" : [ "Wikipedia:Ectoderm" ] + "val" : "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].", + "xrefs" : [ "FMA:9338", "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic ectoderm", - "xrefs" : [ "VHOG:0000153" ] + "pred" : "hasNarrowSynonym", + "val" : "foramen space" } ], "xrefs" : [ { - "val" : "AAO:0000137" - }, { - "val" : "BILA:0000036" - }, { - "val" : "BTO:0000315" - }, { - "val" : "CALOHA:TS-0216" - }, { - "val" : "EFO:0000414" - }, { - "val" : "EHDAA2:0000428" - }, { - "val" : "EMAPA:16069" - }, { - "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" - }, { - "val" : "FMA:69070" - }, { - "val" : "GAID:1304" - }, { - "val" : "MAT:0000155" - }, { - "val" : "MAT:0000173" - }, { - "val" : "MESH:D004475" - }, { - "val" : "MIAA:0000173" - }, { - "val" : "NCIT:C12703" - }, { - "val" : "SCTID:362851007" - }, { - "val" : "TAO:0000016" - }, { - "val" : "UMLS:C0013574" - }, { - "val" : "VHOG:0000153" + "val" : "FMA:9338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "Wikipedia:Ectoderm" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "XAO:0000001" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "ZFA:0000016" - } ], + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", + "lbl" : "main body axis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - 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In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", - "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] + "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", + "xrefs" : [ "CARO:0020001" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neurological system", - "xrefs" : [ "GO:0050877" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "nerve net", - "xrefs" : [ "Wikipedia:Nerve_net" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "systema nervosum", - "xrefs" : [ "Wikipedia:Nervous_system" ] + "val" : "anatomical cluster", + "xrefs" : [ "CARO:0020001" ] } ], "xrefs" : [ { - "val" : "AAO:0000324" - }, { - "val" : "BILA:0000079" - }, { - "val" : "BIRNLEX:844" - }, { - "val" : "BTO:0001484" - }, { - "val" : "CALOHA:TS-1313" - }, { - "val" : "EFO:0000802" - }, { - "val" : "EHDAA2:0001246" - }, { - "val" : "EHDAA:826" - }, { - "val" : "EMAPA:16469" - }, { - "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" - }, { - "val" : "FMA:7157" - }, { - "val" : "GAID:466" - }, { - "val" : "MA:0000016" - }, { - "val" : "MAT:0000026" - }, { - "val" : "MESH:D009420" - }, { - "val" : "MIAA:0000026" - }, { - "val" : "NCIT:C12755" - }, { - "val" : "SCTID:278196006" - }, { - "val" : "TAO:0000396" - }, { - "val" : "UMLS:C0027763" - }, { - "val" : "VHOG:0000402" - }, { - "val" : "WBbt:0005735" + "val" : "CARO:0020001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "Wikipedia:Nervous_system" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "XAO:0000177" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "ZFA:0000396" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", + "lbl" : "disconnected anatomical group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", + "xrefs" : [ "CARO:0020000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "xrefs" : [ { + "val" : "CARO:0020000" }, { - "val" : "neuronames:3236" + "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", + "lbl" : "anatomical collection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "lbl" : "central nervous system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", + "lbl" : "future mouth", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. 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See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "GAID:570" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "val" : "MA:0000167" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "MAT:0000457" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "MESH:D002490" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "NCIT:C12438" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "val" : "SCTID:278199004" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "val" : "TAO:0000012" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" }, { - "val" : "UMLS:C0927232" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { - "val" : "VHOG:0000293" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "Wikipedia:Central_nervous_system" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "val" : "XAO:0000215" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "ZFA:0000012" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "neuronames:854" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001048", - "lbl" : "primordium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].", - "xrefs" : [ "BTO:0001886", "FB:DJS", "FB:FBrf0089570", "http://flybase.org/reports/FBrf0178740.html" ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "bud" - }, { - "pred" : "hasRelatedSynonym", - "val" : "future organ" + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "hasRelatedSynonym", - "val" : "placode", - "xrefs" : [ "FBbt:00005495" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000066" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "primordia", - "xrefs" : [ "XAO:0003043" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" }, { - "pred" : "hasRelatedSynonym", - "val" : "rudiment" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "xrefs" : [ { - "val" : "AEO:0000171" - }, { - "val" : "BTO:0001886" + "val" : "GOREL:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "EFO:0001652" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "xrefs" : [ { + "val" : "GOREL:0002004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "EHDAA2:0003171" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { - "val" : "FBbt:00005495" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "FMA:86589" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "MAT:0000482" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { - "val" : "NCIT:C34275" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "UMLS:C0678727" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "val" : "Wikipedia:Primordium" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "XAO:0003043" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001049", - "lbl" : "neural tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].", - "xrefs" : [ "Wikipedia:Neural_tube" ] + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural primordium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tubus neuralis", - "xrefs" : [ "Wikipedia:Neural_tube" ] - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0010617" - }, { - "val" : "BTO:0001057" - }, { - "val" : "CALOHA:TS-2371" - }, { - "val" : "DHBA:10154" - }, { - "val" : "EHDAA2:0001254" - }, { - "val" : "EHDAA:2869" - }, { - "val" : "EHDAA:908" - }, { - "val" : "EMAPA:16164" - }, { - "val" : "EMAPA:16757" - }, { - "val" : "FMA:293882" - }, { - "val" : "MAT:0000069" - }, { - "val" : "MIAA:0000069" - }, { - "val" : "NCIT:C34226" - }, { - "val" : "SCTID:362852000" - }, { - "val" : "TAO:0001135" - }, { - "val" : "UMLS:C0231024" - }, { - "val" : "VHOG:0000307" - }, { - "val" : "Wikipedia:Neural_tube" - }, { - "val" : "XAO:0003204" - }, { - "val" : "ZFA:0001135" - }, { - "val" : "neuronames:1365" + "val" : "RO:0002007" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", - "lbl" : "anatomical entity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", - "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. 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Consider merging?" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002050", - "lbl" : "embryonic structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that is part of an embryo.", - "xrefs" : [ "BTO:0000174", "ZFIN:curator" ] + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "developing embryonic structure", - "xrefs" : [ "FBbt:00004208" ] - }, { - "pred" : "hasExactSynonym", - "val" : "embryonic anatomical structure", - "xrefs" : [ "RETIRED_EHDAA2:0003169" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonale Struktur", - "xrefs" : [ "BTO:0000174" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "embryonic structures", - "xrefs" : [ "ZFA:0001105" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000138" - }, { - "val" : "BILA:0000034" - }, { - "val" : "BTO:0000174" - }, { - "val" : "CALOHA:TS-2110" - }, { - "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" - }, { - "val" : "FMA:69067" - }, { - "val" : "GAID:407" - }, { - "val" : "MESH:D004628" - }, { - "val" : "NCIT:C13229" - }, { - "val" : "RETIRED_EHDAA2:0003169" - }, { - "val" : "SCTID:667009" - }, { - "val" : "TAO:0001105" - }, { - "val" : "UMLS:C0013948" - }, { - "val" : "VSAO:0000178" - }, { - "val" : "XAO:0003042" - }, { - "val" : "ZFA:0001105" - } ], + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002075", - "lbl" : "viscus", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.", - "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral organ", - "xrefs" : [ "RETIRED_EHDAA2:0002201" ] - }, { - "pred" : "hasExactSynonym", - "val" : "visceral organ system", - "xrefs" : [ "MA:0000019" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic tissue", - "xrefs" : [ "BTO:0001491" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "viscera" - }, { - "pred" : "hasRelatedSynonym", - "val" : "visceral tissue", - "xrefs" : [ "BTO:0001491" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010386" - }, { - "val" : "BTO:0001491" - }, { - "val" : "EHDAA:512" - }, { - "val" : "EMAPA:16245" - }, { - "val" : "FMA:7085" - }, { - "val" : "MA:0000019" - }, { - "val" : "MESH:D014781" - }, { - "val" : "NCIT:C28287" - }, { - "val" : "RETIRED_EHDAA2:0002201" - }, { - "val" : "SCTID:118760003" - }, { - "val" : "UMLS:C0042779" - }, { - "val" : "Wikipedia:Viscus" - }, { - "val" : "XAO:0003034" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", - "lbl" : "postcranial axial skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", - "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, - "comments" : [ "previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "axial skeleton", - "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] - }, { - "pred" : "hasExactSynonym", - "val" : "post-cranial axial skeleton" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0000034" - }, { - "val" : "EFO:0000942" - }, { - "val" : "EHDAA2:0000161" - }, { - "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:37721" - }, { - "val" : "FMA:71221" - }, { - "val" : "MA:0002986" - }, { - "val" : "MAT:0000148" - }, { - "val" : "MIAA:0000148" - }, { - "val" : "TAO:0000317" - }, { - "val" : "VHOG:0000317" - }, { - "val" : "VSAO:0000093" - }, { - "val" : "XAO:0003073" - }, { - "val" : "ZFA:0000317" + "val" : "RO:0002131" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "overlaps" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", - "lbl" : "trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.", - "xrefs" : [ "TAO:0001115", "UBERONREF:0000006", "Wikipedia:Torso" ] + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracolumbar region" - 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"id" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "lbl" : "hemolymphoid system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hematolymphoid system" - }, { - "pred" : "hasExactSynonym", - "val" : "lymphomyeloid complex" - }, { - "pred" : "hasRelatedSynonym", - "val" : "haemolymphoid system" - } ], - "xrefs" : [ { - "val" : "CALOHA:TS-2018" - }, { - "val" : "EHDAA2:0004615" - }, { - "val" : "EMAPA:18765" - }, { - "val" : "FMA:74562" - }, { - "val" : "MA:0000013" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002204", - "lbl" : "musculoskeletal system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of the muscular and skeletal systems.", - "xrefs" : [ "VSAO:0000031", "VSAO:curator", "https://github.com/obophenotype/uberon/issues/77" ] + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "musculo-skeletal system" - } ], - "xrefs" : [ { - "val" : "AAO:0010546" - }, { - "val" : "CALOHA:TS-1311" - 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e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" }, { - "val" : "XAO:0000168" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - 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"val" : "chest cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "pectoral cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "space of thoracic compartment", - "xrefs" : [ "FMA:7565" ] - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic lumen" - } ], - "xrefs" : [ { - "val" : "EMAPA:36497" - }, { - "val" : "FMA:7565" - }, { - "val" : "GAID:93" - }, { - "val" : "MA:0000032" - }, { - "val" : "MESH:D035423" - }, { - "val" : "NCIT:C12905" - }, { - "val" : "SCTID:243949006" - }, { - "val" : "UMLS:C0230139" - }, { - "val" : "Wikipedia:Thoracic_cavity" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", - "lbl" : "coelemic cavity lumen", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.", - "xrefs" : [ "BTO:0001707" ] + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "comments" : [ "EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "body cavity", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity", - "xrefs" : [ "EHDAA2:0000267" ] - }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity lumen", - "xrefs" : [ "EHDAA2:0000267" ] - }, { - "pred" : "hasExactSynonym", - "val" : "main body cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "space of body compartment", - "xrefs" : [ "FMA:85006" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "ventral body cavity", - "xrefs" : [ "NCBITaxon:7742" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "celom", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "coelom" - }, { - "pred" : "hasRelatedSynonym", - "val" : "coelome", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "hemocoel", - "xrefs" : [ "FBbt:00005060" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000186" - }, { - "val" : "BTO:0001707" - }, { - "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" - }, { - "val" : "FMA:85006" - }, { - "val" : "NCIT:C25444" - }, { - "val" : "RETIRED_EHDAA2:0003186" - }, { - "val" : "SCTID:361348008" - }, { - "val" : "TAO:0001438" - }, { - "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" - }, { - "val" : "galen:BodyCavity" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "lbl" : "notochord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A flexible rod-shaped body found in embryos of all chordates. 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In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic notocord" - }, { - "pred" : "hasExactSynonym", - "val" : "notocord", - "xrefs" : [ "ZFA:0000135" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "notochorda", - "xrefs" : [ "Wikipedia:Notochord" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000327" - }, { - "val" : "BTO:0001768" - }, { - "val" : "CALOHA:TS-0690" - }, { - "val" : "EHDAA2:0001277" - }, { - "val" : "EHDAA:1241" - }, { - "val" : "EHDAA:6021" - }, { - "val" : "EMAPA:16191" - }, { - "val" : "EV:0100002" - }, { - "val" : "FMA:85521" - }, { - "val" : "GAID:1311" - }, { - "val" : "MAT:0000281" - }, { - "val" : "MESH:D009672" - }, { - "val" : "NCIT:C12463" - }, { - "val" : "SCTID:308820002" - }, { - "val" : "TAO:0000135" - }, { - "val" : "UMLS:C0028439" - }, { - "val" : "VHOG:0000199" - }, { - "val" : "VSAO:0000032" - }, { - "val" : "Wikipedia:Notochord" - }, { - "val" : "XAO:0000055" - }, { - "val" : "ZFA:0000135" - }, { - "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "lbl" : "somite", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.", - "xrefs" : [ "DOI:10.1111/j.1439-0426.2012.01987.x", "Wikipedia:Somite" ] + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "comments" : [ "When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. 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For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0010578" - }, { - "val" : "BTO:0001764" - }, { - "val" : "CALOHA:TS-0676" - }, { - "val" : "EHDAA2:0004419" - }, { - "val" : "EMAPA:32737" - }, { - "val" : "FMA:86666" - }, { - "val" : "GAID:1310" - }, { - "val" : "MAT:0000066" - }, { - "val" : "MESH:D009432" - }, { - "val" : "MIAA:0000066" - }, { - "val" : "NCIT:C34222" - }, { - "val" : "SCTID:361462002" - }, { - "val" : "UMLS:C0027789" - }, { - "val" : "VHOG:0000057" - }, { - "val" : "Wikipedia:Neural_crest" - }, { - "val" : "XAO:0000048" - }, { - "val" : "ZFA:0000045" - }, { - "val" : "neuronames:1366" + "val" : "RO:0002180" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002346", - "lbl" : "neurectoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Embryonic ectoderm that gives rise to nervous tissue.", - "xrefs" : [ "Wikipedia:Neuroectoderm" ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "This is the transitive form of the develops from relation" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neural ectoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "neuroectoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epithelium tubi neuralis; 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See also: Leydig and epigonal organs" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider placement of NCIT:C53466 medullary bone" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "lbl" : "connective tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue", - "xrefs" : [ "FMA:9640" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bindegewebe", - "xrefs" : [ "BTO:0000421" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0000098" - }, { - "val" : "BTO:0000421" - }, { - "val" : "CALOHA:TS-2009" - }, { - "val" : "EFO:0000952" - }, { - "val" : "EMAPA:35251" - }, { - "val" : "FMA:9640" - }, { - "val" : "GAID:100" - }, { - "val" : "MA:0000011" - }, { - "val" : "MAT:0000301" - }, { - "val" : "MESH:D003238" - }, { - "val" : "MIAA:0000301" - }, { - "val" : "NCIT:C12374" - }, { - "val" : "SCTID:361919005" - }, { - "val" : "TAO:0001641" - }, { - "val" : "UMLS:C0009780" - }, { - "val" : "VSAO:0000017" - }, { - "val" : "XAO:0001017" - }, { - "val" : "ZFA:0001632" - }, { - "val" : "galen:ConnectiveTissue" + "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "lbl" : "muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", - "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, - "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus muscularis" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0000306" - }, { - "val" : "AEO:0000122" - }, { - "val" : "CALOHA:TS-0642" - }, { - "val" : "EHDAA2:0003122" - }, { - "val" : "EMAPA:32715" - }, { - "val" : "FMA:9641" - }, { - "val" : "MA:0002437" - }, { - "val" : "MESH:D009132" - }, { - "val" : "NCIT:C12435" - }, { - "val" : "SCTID:91727004" - }, { - "val" : "UMLS:C2328219" - }, { - "val" : "Wikipedia:Muscle_tissue" - }, { - "val" : "galen:MuscleTissue" + "val" : "RO:0002215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - 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This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011003" - }, { - "val" : "BILA:0000104" - }, { - "val" : "BTO:0005810" - }, { - "val" : "FMA:9825" - }, { - "val" : "GAID:328" - }, { - "val" : "MA:0002711" - }, { - "val" : "MESH:D007107" - }, { - "val" : "NCIT:C12735" - }, { - "val" : "SCTID:362590003" - }, { - "val" : "TAO:0001159" - }, { - "val" : "UMLS:C0020962" - }, { - "val" : "VHOG:0001247" - }, { - "val" : "Wikipedia:Immune_system" - }, { - "val" : "XAO:0003152" - }, { - "val" : "ZFA:0001159" + "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "lbl" : "bone tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000047", "http://dx.plos.org/10.1371/journal.pone.0051070" ] + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "calcium tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "osseous tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "osteogenic tissue", - "xrefs" : [ "VSAO:curator" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "mineralized bone tissue", - "xrefs" : [ "XAO:0004040" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "bone", - "xrefs" : [ "MESH:A02.835.232" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "portion of bone tissue", - "xrefs" : [ "FMA:224804" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "CALOHA:TS-2011" - }, { - "val" : "EMAPA:35179" - }, { - "val" : "FMA:224804" - }, { - "val" : "MA:0002780" - }, { - "val" : "MESH:D001842" - }, { - "val" : "NCIT:C13076" - }, { - "val" : "UMLS:C0391978" - }, { - "val" : "VSAO:0000047" - }, { - "val" : "Wikipedia:Bone_tissue" - }, { - "val" : "XAO:0004040" - }, { - "val" : "ZFA:0005621" - }, { - "val" : "galen:BoneTissue" + "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "see https://github.com/obophenotype/uberon/issues/27" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", - "lbl" : "epiblast (generic)", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", - "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epiblast", - "xrefs" : [ "VHOG:0000243" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocyst" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ectoblast", - "xrefs" : [ "MP:0003886" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epiblastus", - "xrefs" : [ "Wikipedia:Epiblast" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "primitive ectoderm", - "xrefs" : [ "VHOG:0000243" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BTO:0004593" - }, { - "val" : "FMA:296704" - }, { - "val" : "MAT:0000067" - }, { - "val" : "MIAA:0000067" - }, { - "val" : "VHOG:0000243" - }, { - "val" : "Wikipedia:Epiblast" + "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" - }, { - "val" : "NCIT:C34007" - }, { - "val" : "galen:Cavity" + "val" : "RO:0002232" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "segmental plate" - }, { - "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" - }, { - "val" : "XAO:0000057" - }, { - "val" : "ZFA:0000279" + "val" : "RO:0002233" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", - "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ventral lateral plate mesoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "blood islands" - }, { - "pred" : "hasRelatedSynonym", - "val" : "VBI" - }, { - "pred" : "hasRelatedSynonym", - "val" : "caudal hematopoietic tissue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior ICM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior blood island" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral blood island" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011006" - }, { - "val" : "EFO:0003489" - }, { - "val" : "EHDAA:207" - }, { - "val" : "NCIT:C34113" - }, { - "val" : "TAO:0000094" - }, { - "val" : "TE:E5.11.2.0.0.0.4" - }, { - "val" : "UMLS:C1511224" - }, { - "val" : "VHOG:0000085" - }, { - "val" : "Wikipedia:Blood_island_of_umbilical_vesicle" - }, { - "val" : "XAO:0000067" - }, { - "val" : "ZFA:0000094" + "val" : "RO:0002234" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "lbl" : "axial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.", - "xrefs" : [ "GO:0048318", "Wikipedia:Chordamesoderm" ] + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm", - "xrefs" : [ "Wikipedia:Chordamesoderm" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011017" - }, { - "val" : "EFO:0003647" - }, { - "val" : "TAO:0001204" - }, { - "val" : "VHOG:0000107" - }, { - "val" : "Wikipedia:Chordamesoderm" - }, { - "val" : "XAO:0000205" - }, { - "val" : "ZFA:0001204" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "lbl" : "neural plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A region of embryonic ectodermal cells that lie directly above the notochord. 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"pred" : "hasRelatedSynonym", - "val" : "mesenchyma", - "xrefs" : [ "Wikipedia:Mesenchyme" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0010427" - }, { - "val" : "AEO:0000145" - }, { - "val" : "BTO:0001393" - }, { - "val" : "CALOHA:TS-0620" - }, { - "val" : "EHDAA2:0003145" - }, { - "val" : "EV:0100007" - }, { - "val" : "NCIT:C13301" - }, { - "val" : "TAO:0000393" - }, { - "val" : "UMLS:C0162415" - }, { - "val" : "VHOG:0000170" - }, { - "val" : "Wikipedia:Mesenchyme" - }, { - "val" : "XAO:0003046" - }, { - "val" : "ZFA:0000393" + "val" : "RO:0002305" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "lbl" : "future coelemic cavity lumen", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future coelomic cavity lumen" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" }, { - "pred" : "hasRelatedSynonym", - "val" : "body cavity precursor" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002315" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", - "lbl" : "intraembryonic coelom", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", - "xrefs" : [ "MGI:anna", "MP:0012187" ] + "val" : "A relationship that holds via some environmental process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "somatic coelom", - "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] - } ], "xrefs" : [ { - "val" : "EHDAA:251" - }, { - "val" : "EMAPA:16088" - }, { - "val" : "NCIT:C34195" - }, { - "val" : "UMLS:C1512940" - }, { - "val" : "VHOG:0000316" - }, { - "val" : "Wikipedia:Intraembryonic_coelom" + "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", - "lbl" : "epithelial tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", - "xrefs" : [ "GO:0060562", "PMID:12526790" ] + "val" : "inverse of regulates" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial or endothelial tube" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "xrefs" : [ { - "val" : "AEO:0000114" - }, { - "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" + "val" : "RO:0002334" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004111", - "lbl" : "anatomical conduit", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any tube, opening or passage that connects two distinct anatomical spaces.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "inverse of negatively regulates" }, - 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}, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" } ] } }, { - 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"pred" : "hasExactSynonym", - "val" : "mesodermal derivative", - "xrefs" : [ "FBbt:00025998" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004121", - "lbl" : "ectoderm-derived structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical structure that develops (entirely or partially) from the ectoderm.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ectodermal deriviative", - "xrefs" : [ "FBbt:00025990" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", - "lbl" : "cardiogenic plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The first recognizable structure derived from the heart field.", - "xrefs" : [ "GO:0003142" ] + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "myocardial plate", - "xrefs" : [ "EHDAA2:0000215" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac crescent", - "xrefs" : [ "EMAPA:16106" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiogenic crescent", - "xrefs" : [ "GO:0003142" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "heart rudiment" - } ], "xrefs" : [ { - "val" : "EHDAA2:0000215" - }, { - "val" : "EMAPA:16106" - }, { - "val" : "VHOG:0000975" + "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", - "lbl" : "primary heart field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", - "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "first heart field", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primary heart field", - "xrefs" : [ "PMID:17276708", "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "FHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "PHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "heart field", - "xrefs" : [ "XAO:0004185" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { - "val" : "XAO:0004185" + "val" : "RO:0002342" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", - "lbl" : "heart tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An epithelial tube that will give rise to the mature heart.", - "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic heart tube", - "xrefs" : [ "GO:0003143" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial heart tube", - "xrefs" : [ "MP:0012700" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial tube", - "xrefs" : [ "XAO:0000337" ] - } ], "xrefs" : [ { - "val" : "AAO:0010411" - }, { - "val" : "EFO:0003526" - }, { - "val" : "EMAPA:32685" - }, { - "val" : "NCIT:C34161" - }, { - "val" : "TAO:0000360" - }, { - "val" : "XAO:0000337" - }, { - "val" : "ZFA:0000360" + "val" : "RO:0002343" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", - "lbl" : "cardiac chamber", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", - "xrefs" : [ "GO:0003205" ] - }, - "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chamber of heart" - }, { - "pred" : "hasExactSynonym", - "val" : "heart chamber" - } ], "xrefs" : [ { - "val" : "FMA:7095" - }, { - "val" : "SCTID:276456008" + "val" : "RO:0002344" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_to_from_or_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "is member of is a mereological relation between a item and a collection." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "set of all bones" - }, { - "pred" : "hasExactSynonym", - "val" : "set of bones of body" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AEO:0000168" - }, { - "val" : "EHDAA2:0001843" - }, { - "val" : "EHDAA:5047" - }, { - "val" : "EMAPA:17213" - }, { - "val" : "FMA:23875" - }, { - "val" : "GAID:177" - }, { - "val" : "MA:0003006" - }, { - "val" : "MAT:0000032" - }, { - "val" : "MESH:D012863" - }, { - "val" : "MIAA:0000032" - }, { - "val" : "SCTID:361378004" - }, { - "val" : "VSAO:0000026" - }, { - "val" : "Wikipedia:Skeleton" - }, { - "val" : "XAO:0004053" - }, { - "val" : "galen:Skeleton" + "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "output_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" + "val" : "http://dbpedia.org/property/origin" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004291", - "lbl" : "heart rudiment", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.", - "xrefs" : [ "GO:0003313" ] + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart cone", - "xrefs" : [ "GO:0003313" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rudimentary heart", - "xrefs" : [ "ZFA:0000115" ] - } ], - "xrefs" : [ { - "val" : "TAO:0000115" - }, { - "val" : "ZFA:0000115" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "lbl" : "cardiovascular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that has as its parts the heart and blood vessels.", - "xrefs" : [ "BTO:0000088" ] + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "CV system", - "xrefs" : [ "BTO:0000088" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Herz und Gefaesssystem", - "xrefs" : [ "BTO:0000088" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011001" - }, { - "val" : "BILA:0000016" - }, { - "val" : "BTO:0000088" - }, { - "val" : "CALOHA:TS-1297" - }, { - "val" : "EFO:0000791" - }, { - "val" : "EHDAA:394" - }, { - "val" : "EMAPA:16104" - }, { - "val" : "EV:0100017" - }, { - "val" : "FMA:7161" - }, { - "val" : "GAID:467" - }, { - "val" : "MA:0000010" - }, { - "val" : "MAT:0000016" - }, { - "val" : "MESH:D002319" - }, { - "val" : "MIAA:0000016" - }, { - "val" : "NCIT:C12686" - }, { - "val" : "SCTID:278198007" - }, { - "val" : "TAO:0000010" - }, { - "val" : "UMLS:C0007226" - }, { - "val" : "VHOG:0000302" - }, { - "val" : "WikipediaCategory:Cardiovascular_system" - }, { - "val" : "XAO:0000100" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { - "val" : "XAO:0001010" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" }, { - "val" : "ZFA:0000010" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "lbl" : "blood vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A vascular network consisting of blood vessels.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "inverse of upstream of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blood vascular network" - }, { - "pred" : "hasExactSynonym", - "val" : "set of blood vessels" - }, { - "pred" : "hasRelatedSynonym", - "val" : "blood system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "blood vessel system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "blood vessels", - "xrefs" : [ "TAO:0001079" ] - } ], "xrefs" : [ { - "val" : "TAO:0001079" - }, { - "val" : "ZFA:0001079" + "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004638", - "lbl" : "blood vessel endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "xrefs" : [ { - "val" : "BTO:0000766" - }, { - "val" : "CALOHA:TS-2155" - }, { - "val" : "EMAPA:35176" - }, { - "val" : "MA:0000709" - }, { - "val" : "NCIT:C53395" - }, { - "val" : "TAO:0005257" - }, { - "val" : "UMLS:C1706972" - }, { - "val" : "ZFA:0005257" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004716", - "lbl" : "conceptus", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].", - "xrefs" : [ "BTO:0003834", "Wikipedia:Conceptus" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryo plus adnexa" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AEO:0000194" - }, { - "val" : "BTO:0003834" - }, { - "val" : "EHDAA2:0000001" - }, { - "val" : "EHDAA2:0003235" - }, { - "val" : "EMAPA:36040" - }, { - "val" : "NCIT:C34131" - }, { - "val" : "UMLS:C1516779" - }, { - "val" : "Wikipedia:Conceptus" + "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", - "lbl" : "gastrula", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the gastrula stage.", - "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gastrula embryo", - "xrefs" : [ "BILA:0000060" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocystis trilaminaris", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastocyst", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "trilaminar germ", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "BILA:0000060" - }, { - "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" - }, { - "val" : "FMA:293108" - }, { - "val" : "GAID:1302" - }, { - "val" : "MESH:D005775" - }, { - "val" : "MIAA:0000179" - }, { - "val" : "NCIT:C34057" - }, { - "val" : "NCIT:C34058" - }, { - "val" : "UMLS:C0017199" - }, { - "val" : "UMLS:C1284022" - }, { - "val" : "Wikipedia:Gastrula" - }, { - "val" : "Wikipedia:Trilaminar_blastocyst" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004755", - "lbl" : "skeletal tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000015", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/134" ] + "val" : "inverse of causally upstream of or within" }, - "comments" : [ "Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "xrefs" : [ { - "val" : "EMAPA:37744" - }, { - "val" : "MA:0003047" - }, { - "val" : "SCTID:309311006" - }, { - "val" : "VSAO:0000015" - }, { - "val" : "XAO:0004038" - }, { - "val" : "ZFA:0005619" + "val" : "RO:0002427" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", - "lbl" : "skeletal element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" - }, { - "val" : "galen:SkeletalStructure" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" - }, { - "val" : "MA:0003007" - }, { - "val" : "SCTID:361827000" - }, { - "val" : "VSAO:0000181" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", - "lbl" : "cardiovascular system endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that is part of the cardiovascular system.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "endothelia", - "xrefs" : [ "ZFA:0001639" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "vascular endothelia", - "xrefs" : [ "XAO:0000356" ] - } ], - "xrefs" : [ { - "val" : "BTO:0001853" - }, { - "val" : "EMAPA:35201" - }, { - "val" : "GAID:519" - }, { - "val" : "MA:0000717" - }, { - "val" : "MESH:D004730" - }, { - "val" : "NCIT:C13053" - }, { - "val" : "TAO:0002171" - }, { - "val" : "UMLS:C0014261" - }, { - "val" : "VHOG:0001217" - }, { - "val" : "XAO:0000356" - }, { - "val" : "ZFA:0001639" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004872", - "lbl" : "splanchnic layer of lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "visceral mesoderm", - "xrefs" : [ "BILA:0000044", "http://www.drugs.com/dict/visceral-mesoderm.html", "http://www.stedmans.com/" ] - }, { - "pred" : "hasExactSynonym", - "val" : "inner layer of lateral plate mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011102" - }, { - "val" : "BILA:0000044" - }, { - "val" : "FMA:295568" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" - }, { - "val" : "XAO:0000276" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000478" - }, { - "val" : "EFO:0003426" - }, { - "val" : "TAO:0000091" - }, { - "val" : "ZFA:0000091" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004905", - "lbl" : "articulation", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A proximal-distal subdivision of the digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system subdivision", - "xrefs" : [ "FMA:71131" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut section", - "xrefs" : [ "FBbt:00100315" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "segment of intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "subdivision of alimentary system", - "xrefs" : [ "FMA:71131" ] - } ], - "xrefs" : [ { - "val" : "FBbt:00100315" - }, { - "val" : "FMA:71131" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "lbl" : "organ component layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A part of a wall of an organ that forms a layer.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FMA:82485" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005061", - "lbl" : "neural groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.", - "xrefs" : [ "GO:0001842", "Wikipedia:Neural_groove", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. 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The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "lbl" : "neural fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "One of the two elevated edges of the neural groove[GO,MP].", - "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. 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X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", - "lbl" : "meso-epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesoderm-derived epithelium" - }, { - "pred" : "hasExactSynonym", - "val" : "mesoepithelium" - } ], - "xrefs" : [ { - "val" : "FMA:86452" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012429", - "lbl" : "hematopoietic tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", + "lbl" : "transitively distally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Blood-forming tissue, consisting of reticular fibers and cells.", - "xrefs" : [ "http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue" ] - 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Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", - "lbl" : "body proper", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "The region of the organism associated with the visceral organs.", - "xrefs" : [ "AEO:0000103" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "body", - "xrefs" : [ "AEO:0000103" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "whole body", - "xrefs" : [ "BTO:0001489" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000103" - }, { - "val" : "BTO:0001489" - }, { - "val" : "FMA:231424" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", - "lbl" : "thoracic skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", - "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "skeleton of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic part of axial skeleton" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic skeleton", - "xrefs" : [ "EHDAA2:0002013" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002013" - }, { - "val" : "FMA:77169" - }, { - "val" : "Wikipedia:Thoracic_skeleton" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", - "lbl" : "primordial vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A portion of tissue that will develop into vasculature.", - "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "xrefs" : [ { - "val" : "EFO:0003708" - }, { - "val" : "TAO:0005076" - }, { - "val" : "ZFA:0005076" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015203", - "lbl" : "non-connected functional system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An anatomical group whose component structures share a common function.", - "xrefs" : [ "AEO:0000093", "AEO:JB", "FBC:DOS", "FBbt:00007278" ] + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, - "xrefs" : [ { - "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "lbl" : "lateral structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", - "lbl" : "circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "heart" - }, { - "pred" : "hasExactSynonym", - "val" : "cardiac pump" - }, { - "pred" : "hasExactSynonym", - "val" : "heart or heart like organ" - }, { - "pred" : "hasNarrowSynonym", - "val" : "circulatory vessel" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac structure" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", - "lbl" : "heart plus pericardium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart/pericardium", - "xrefs" : [ "MA:0002449" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37597" - }, { - "val" : "MA:0002449" - } ], + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015757", - "lbl" : "heterogeneous tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of heterogeneous tissue", - "xrefs" : [ "FMA:62798" ] - } ], - "xrefs" : [ { - "val" : "FMA:62798" - } ], + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", - "lbl" : "future central nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Primordium that develops into the central nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future CNS" - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive central nervous system" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", - "lbl" : "future nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Primordium that develops into the nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive nervous system", - "xrefs" : [ "AAO:0000477" ] - } ], + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "xrefs" : [ { - "val" : "AAO:0000477" + "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016887", - "lbl" : "entire extraembryonic component", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", - "xrefs" : [ "AEO:0000195", "AEO:JB" ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "extra-embryonic component" - }, { - "pred" : "hasExactSynonym", - "val" : "extraembryonic component", - "xrefs" : [ "AEO:0000195" ] - } ], "xrefs" : [ { - "val" : "AEO:0000195" - }, { - "val" : "EHDAA2:0000003" - }, { - "val" : "EMAPA:16042" + "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034769", - "lbl" : "lymphomyeloid tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "xrefs" : [ { - "val" : "FMA:79770" - }, { - "val" : "NCIT:C41168" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], - "xrefs" : [ { - "val" : "CARO:0020001" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] + "val" : "A synonym type for describing abbreviations or initalisms" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A synonym type for describing pluralization synonyms" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], - "xrefs" : [ { - "val" : "FMA:293105" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036146", - "lbl" : "cardiopharyngeal field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.", - "xrefs" : [ "http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1", "https://orcid.org/0000-0003-3308-6245" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { @@ -31460,6 +31957,7 @@ "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } @@ -31467,49 +31965,15 @@ "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { @@ -31517,291 +31981,391 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", "lbl" : "latin term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", "lbl" : "plural term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "type" : "PROPERTY", - "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." - }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "type" : "PROPERTY", - "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -31817,11 +32381,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -31838,6 +32404,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -31853,11 +32420,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -31873,23 +32442,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -31899,6 +32497,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -32134,16 +32744,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000483" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000076", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "is_a", @@ -32392,8 +32992,8 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000213" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000133", "pred" : "is_a", @@ -34416,14 +35016,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002077", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000221" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000066" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002078", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002087", "pred" : "is_a", @@ -35994,10 +36586,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044249" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009059", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_1901576" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009605", "pred" : "is_a", @@ -37778,10 +38366,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0070925", "pred" : "http://purl.obolibrary.org/obo/RO_0002588", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0071704", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0071707", "pred" : "is_a", @@ -38138,14 +38722,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140546", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0098542" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1902105", "pred" : "is_a", @@ -38582,6 +39158,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070047", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0070045" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -38926,6 +39514,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000040662", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000025", "pred" : "is_a", @@ -43232,6 +43824,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -43334,10 +43930,10 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000071", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000076" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0004638" + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000080", @@ -44559,13 +45155,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000221" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002078", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", - "fillerId" : "http://purl.obolibrary.org/obo/CL_0000222" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002087", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000738" ], @@ -46850,6 +47439,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.obo b/src/ontology/subsets/blood_and_immune_upper_slim.obo index 5f0fdb066..ad7ec0937 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.obo +++ b/src/ontology/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -119,7 +124,7 @@ relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] @@ -133,7 +138,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -158,7 +163,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -206,7 +211,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -222,7 +227,7 @@ synonym: "colony forming unit monocyte" RELATED [] synonym: "monocyte stem cell" RELATED [] xref: CALOHA:TS-1195 xref: FMA:83553 -xref: ZFA:0009017 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -246,7 +251,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -269,7 +274,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor @@ -290,7 +295,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -319,7 +324,7 @@ synonym: "early lymphocyte progenitor" RELATED [] synonym: "ELP" RELATED OMO:0003000 [] synonym: "lymphoid stem cell" RELATED [] synonym: "lymphopoietic stem cell" RELATED [] -xref: ZFA:0009023 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009023 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell @@ -334,7 +339,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -354,10 +359,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -373,7 +378,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -389,14 +394,14 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -405,12 +410,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -420,14 +423,14 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] -xref: ZFA:0009043 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid @@ -441,7 +444,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -464,7 +467,7 @@ xref: CALOHA:TS-1001 xref: FMA:62870 xref: MESH:D013601 xref: VHOG:0001479 -xref: ZFA:0009046 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009046 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000542 {is_inferred="true"} ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity @@ -484,7 +487,7 @@ xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 xref: MESH:D010010 -xref: ZFA:0009047 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell @@ -521,7 +524,7 @@ xref: BTO:0000539 xref: BTO:0001026 xref: CALOHA:TS-0422 xref: FMA:62854 -xref: ZFA:0009048 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte @@ -596,7 +599,7 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 -xref: ZFA:0009064 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) @@ -614,9 +617,9 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -624,7 +627,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -648,7 +651,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -661,7 +664,7 @@ comment: Note change of name; nearly all somatic cells can present antigens to T subset: blood_and_immune_upper_slim subset: cellxgene_subset synonym: "APC" RELATED OMO:0003000 [] -xref: ZFA:0009088 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II @@ -696,20 +699,20 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -717,21 +720,21 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -743,7 +746,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -755,7 +758,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -765,7 +768,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -862,7 +865,7 @@ subset: cellxgene_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 -xref: ZFA:0009140 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009140 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000473 ! defensive cell @@ -885,7 +888,7 @@ xref: CALOHA:TS-0587 xref: FMA:63261 xref: FMA:83585 xref: MESH:D008264 -xref: ZFA:0009141 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009141 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte @@ -913,7 +916,7 @@ xref: CALOHA:TS-0068 xref: FMA:62869 xref: MESH:D001402 xref: VHOG:0001480 -xref: ZFA:0009142 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009142 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity @@ -942,7 +945,7 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -953,7 +956,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -963,7 +966,7 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -991,14 +994,14 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1014,7 +1017,7 @@ xref: BTO:0002042 xref: CALOHA:TS-0194 xref: FMA:83036 xref: MESH:D003713 -xref: ZFA:0009209 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell intersection_of: CL:0000738 ! leukocyte @@ -1043,7 +1046,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000457 name: biogenic amine secreting cell -xref: ZFA:0009212 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009212 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] @@ -1052,7 +1055,7 @@ name: serotonin secreting cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] -xref: ZFA:0009213 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001820 ! serotonin secretion @@ -1083,16 +1086,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1107,7 +1110,7 @@ xref: CALOHA:TS-0583 xref: FMA:62863 xref: MESH:D008214 xref: VHOG:0001535 -xref: ZFA:0009250 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009250 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -1175,7 +1178,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -1196,7 +1199,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -1314,7 +1317,7 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] -xref: ZFA:0009251 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell @@ -1346,7 +1349,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -1386,7 +1389,7 @@ subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0004657 xref: FMA:83551 -xref: ZFA:0009253 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -1405,7 +1408,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1429,7 +1432,7 @@ subset: human_reference_atlas xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 -xref: ZFA:0009265 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009265 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0011026 ! progenitor cell @@ -1473,7 +1476,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1486,7 +1489,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1506,7 +1509,7 @@ xref: CALOHA:TS-0549 xref: FMA:62852 xref: MESH:D007962 xref: NCIT:C12529 -xref: ZFA:0009309 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009309 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell @@ -1526,7 +1529,7 @@ name: nucleated thrombocyte def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. subset: blood_and_immune_upper_slim -xref: ZFA:0009323 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell intersection_of: CL:0000763 ! myeloid cell @@ -1543,7 +1546,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1560,7 +1563,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -1575,7 +1578,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -1614,7 +1617,7 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009326 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte @@ -1704,7 +1707,7 @@ xref: BTO:0000130 xref: CALOHA:TS-0688 xref: FMA:62860 xref: MESH:D009504 -xref: ZFA:0009327 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009327 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II @@ -1764,7 +1767,7 @@ subset: cellxgene_subset synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] -xref: ZFA:0009331 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009331 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive @@ -1795,7 +1798,7 @@ synonym: "plasmocyte" EXACT [] xref: BTO:0000392 xref: FMA:70574 xref: MESH:D010950 -xref: ZFA:0009332 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex @@ -1822,7 +1825,7 @@ subset: cellxgene_subset synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] -xref: ZFA:0009335 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex @@ -1842,7 +1845,7 @@ synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] -xref: ZFA:0009336 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -1861,7 +1864,7 @@ synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] synonym: "newly formed B cell" EXACT [ISBN:781735149] -xref: ZFA:0009343 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009343 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030044 GO:0045190 ! has_not_completed isotype switching @@ -1884,7 +1887,7 @@ subset: human_reference_atlas synonym: "pre-B cell" RELATED [] xref: BTO:0001133 xref: CALOHA:TS-0819 -xref: ZFA:0009344 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009344 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex @@ -1908,7 +1911,7 @@ synonym: "transitional B cell" EXACT [PMID:22343568] synonym: "transitional stage B lymphocyte" EXACT [] synonym: "transitional stage B-cell" EXACT [] synonym: "transitional stage B-lymphocyte" EXACT [] -xref: ZFA:0009345 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009345 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030044 GO:0002335 ! has_not_completed mature B cell differentiation @@ -1941,7 +1944,7 @@ synonym: "progenitor B lymphocyte" EXACT [] synonym: "progenitor B-cell" EXACT [] synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 -xref: ZFA:0009349 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 @@ -1963,7 +1966,7 @@ synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] synonym: "progenitor T cell" EXACT [] synonym: "TN1 cell" NARROW [] -xref: ZFA:0009350 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009350 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation @@ -1975,7 +1978,7 @@ id: CL:0000828 name: thromboblast def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. -xref: ZFA:0009351 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009351 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell @@ -2059,7 +2062,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -2106,7 +2109,7 @@ synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 xref: FMA:70338 -xref: ZFA:0009355 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009355 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -2125,7 +2128,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -2144,7 +2147,7 @@ synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 xref: CALOHA:TS-0768 xref: FMA:86713 -xref: ZFA:0009357 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009357 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte @@ -2261,7 +2264,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -2301,8 +2304,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 creation_date: 2011-11-16T04:28:16Z [Term] @@ -2336,7 +2339,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2356,9 +2359,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:20:48Z" xsd:dateTime [Term] id: CL:0001200 @@ -2373,7 +2376,7 @@ intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001201 @@ -2390,7 +2393,7 @@ intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0002009 @@ -2407,7 +2410,7 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -2437,7 +2440,7 @@ relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T12:46:33Z [Term] @@ -2451,7 +2454,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -2465,7 +2468,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2473,28 +2476,14 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z -[Term] -id: CL:0002078 -name: meso-epithelial cell -def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] -synonym: "epithelial mesenchymal cell" EXACT [] -xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000066 ! epithelial cell -intersection_of: CL:0000066 ! epithelial cell -intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell -relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2010-06-29T03:49:14Z - [Term] id: CL:0002087 name: nongranular leukocyte @@ -2506,7 +2495,7 @@ is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: CL:4030045 GO:0030141 ! lacks_part secretory granule relationship: CL:4030045 GO:0030141 ! lacks_part secretory granule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T11:30:33Z [Term] @@ -2522,7 +2511,7 @@ is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -2537,7 +2526,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -2550,7 +2539,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T12:54:27Z [Term] @@ -2562,7 +2551,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -2574,7 +2563,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -2585,7 +2574,7 @@ is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion relationship: capable_of GO:0001821 ! histamine secretion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:04:42Z [Term] @@ -2599,7 +2588,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -2610,12 +2599,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -2625,9 +2614,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -2643,7 +2632,7 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0045058 ! has_not_completed T cell selection -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:17Z [Term] @@ -2660,7 +2649,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -2668,9 +2657,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -2700,7 +2689,7 @@ relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like pr relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-29T10:08:02Z [Term] @@ -2710,18 +2699,18 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2768,7 +2757,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2791,7 +2780,7 @@ xref: EFO:0000572 xref: FMA:83030 is_a: CL:0000542 ! lymphocyte relationship: output_of GO:0046649 ! lymphocyte activation -property_value: http://purl.org/dc/elements/1.1/date "2022-08-17T14:20:01Z" xsd:string +property_value: dc:date "2022-08-17T14:20:01Z" xsd:string created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -2803,7 +2792,7 @@ xref: EFO:0005293 xref: FMA:83031 is_a: CL:0000945 ! lymphocyte of B lineage is_a: CL:0017005 ! lymphoblast -property_value: http://purl.org/dc/elements/1.1/date "2022-08-17T14:30:32Z" xsd:string +property_value: dc:date "2022-08-17T14:30:32Z" xsd:string created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -2814,7 +2803,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2826,7 +2815,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2837,7 +2826,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2848,7 +2837,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2856,7 +2845,7 @@ id: CL:0017508 name: cartwheel heterochromatin def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:28:35Z [Term] @@ -2882,7 +2871,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0000178 ! blood relationship: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-11T17:29:04Z [Term] @@ -2894,14 +2883,14 @@ is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/date "2022-11-04T14:40:00Z" xsd:dateTime +property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -3928,7 +3917,7 @@ alt_id: GO:0001623 alt_id: GO:0001624 alt_id: GO:0001625 alt_id: GO:0016526 -def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR] +def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, Wikipedia:GPCR] subset: goslim_chembl synonym: "EBV-induced receptor" NARROW [] synonym: "Epstein-Barr Virus-induced receptor activity" NARROW [] @@ -4459,7 +4448,7 @@ name: exocytosis namespace: biological_process alt_id: GO:0016194 alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] +def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] synonym: "vesicle exocytosis" EXACT [] @@ -4998,7 +4987,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -5606,7 +5594,7 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -5621,7 +5609,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -5634,7 +5622,7 @@ relationship: results_in_assembly_of GO:0042995 ! cell projection id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -6610,7 +6598,7 @@ is_a: GO:0042611 ! MHC protein complex id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -6842,13 +6830,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -7961,20 +7950,6 @@ relationship: results_in_assembly_of GO:0043226 ! organelle created_by: mah creation_date: 2009-09-15T03:00:51Z -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071707 name: immunoglobulin heavy chain V-D-J recombination @@ -8504,27 +8479,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2020-11-11T17:19:06Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1902105 name: regulation of leukocyte differentiation @@ -9325,7 +9279,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -9335,7 +9289,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -9347,7 +9301,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -9357,7 +9311,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -9366,7 +9320,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -9379,7 +9333,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -9389,7 +9343,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -9402,7 +9356,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -9413,7 +9367,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -9422,7 +9376,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -9484,6 +9438,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -10592,6 +10549,15 @@ synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -10648,6 +10614,18 @@ synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -10718,7 +10696,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -11024,7 +11002,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -11126,7 +11104,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -11150,7 +11128,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -11209,7 +11187,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -11232,7 +11210,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -11292,7 +11270,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -11327,7 +11305,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -11355,7 +11333,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -11380,7 +11358,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -11417,7 +11395,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -11471,7 +11449,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -11515,7 +11493,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -11551,7 +11529,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -11571,7 +11549,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -11598,7 +11576,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -11633,7 +11611,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -11666,7 +11644,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -11687,7 +11665,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -11716,7 +11694,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000490 @@ -11787,7 +11765,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -11808,7 +11786,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -11828,7 +11806,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -11862,7 +11840,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -11880,7 +11858,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -11900,7 +11878,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -11917,8 +11895,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -11944,7 +11922,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -11961,7 +11939,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -11984,7 +11962,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -11997,7 +11975,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -12052,9 +12030,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -12119,7 +12097,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -12169,7 +12147,7 @@ disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -12208,7 +12186,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -12234,7 +12212,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -12262,8 +12240,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -12294,7 +12272,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -12334,7 +12312,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -12381,7 +12359,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -12397,7 +12375,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -12522,7 +12500,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -12653,7 +12631,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -12702,7 +12680,7 @@ is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -12724,7 +12702,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -12916,8 +12894,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -12941,7 +12919,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12998,7 +12976,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -13039,7 +13017,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -13081,8 +13059,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -13105,7 +13083,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -13163,7 +13141,7 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -13364,7 +13342,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -13463,7 +13441,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -13498,7 +13476,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -13529,7 +13507,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -13564,7 +13542,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13614,7 +13592,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -13670,7 +13648,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -13716,7 +13694,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -13952,8 +13930,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -14018,7 +13996,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14158,7 +14136,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14174,7 +14152,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -14360,7 +14338,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -14464,7 +14442,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -14865,7 +14843,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -14949,7 +14927,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -15069,7 +15047,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -15255,7 +15233,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -15376,7 +15354,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -16489,8 +16467,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16498,8 +16476,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16508,8 +16486,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -16660,16 +16638,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -16678,6 +16660,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -16695,6 +16678,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -16913,6 +16897,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -17371,18 +17356,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.owl b/src/ontology/subsets/blood_and_immune_upper_slim.owl index 2a51bb253..bb770b572 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.owl +++ b/src/ontology/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4511,6 +4517,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4522,6 +4530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4532,6 +4541,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4544,6 +4554,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4562,6 +4573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4591,6 +4603,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4699,6 +4712,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4710,6 +4724,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4721,6 +4736,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -5710,15 +5726,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - @@ -5735,17 +5750,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -6468,7 +6476,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -12441,7 +12454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A connective tissue cell found in bone. - 2011-11-16T04:28:16Z + 2011-11-16T04:28:16Z bone cell @@ -12593,7 +12606,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative @@ -12816,7 +12829,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. - 2010-01-19T02:51:58Z + 2010-01-19T02:51:58Z MDP macrophage dendritic cell progenitor @@ -12937,7 +12950,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa - 2010-04-27T12:46:33Z + 2010-04-27T12:46:33Z BMCP There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. @@ -12985,7 +12998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -13028,7 +13041,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -13067,7 +13080,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -13088,51 +13101,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - Epithelial cell derived from mesoderm or mesenchyme. - - 2010-06-29T03:49:14Z - FMA:69076 - ZFA:0009388 - epithelial mesenchymal cell - meso-epithelial cell - - - - - Epithelial cell derived from mesoderm or mesenchyme. - FMA:69076 - GOC:tfm - - - - - ZFA:0009388 - - - - - @@ -13156,7 +13124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A leukocyte that lacks granules. - 2010-07-22T11:30:33Z + 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte @@ -13200,7 +13168,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. - 2010-07-22T04:48:15Z + 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 @@ -13230,7 +13198,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -13274,7 +13242,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell involved in the formation of a granulocyte. - 2010-08-30T12:54:27Z + 2010-08-30T12:54:27Z FMA:83519 granulocytopoietic cell @@ -13317,7 +13285,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell involved in the formation of a monocyte (monopoiesis). - 2010-08-30T01:27:48Z + 2010-08-30T01:27:48Z FMA:83552 monopoietic cell @@ -13359,7 +13327,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -13395,7 +13363,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell type that secretes histamine. - 2010-09-10T03:04:42Z + 2010-09-10T03:04:42Z histamine secreting cell @@ -13430,7 +13398,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -13469,7 +13437,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -13499,7 +13467,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -13544,7 +13512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A T cell that has not completed T cell selection. - 2010-10-12T01:56:17Z + 2010-10-12T01:56:17Z BTO:0001372 CALOHA:TS-1042 immature T-cell @@ -13590,7 +13558,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -13614,7 +13582,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -13747,7 +13715,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13 - 2011-08-29T10:08:02Z + 2011-08-29T10:08:02Z natural helper lymphocyte @@ -13773,7 +13741,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). - 2012-06-15T02:51:27Z + 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -13811,7 +13779,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -14050,7 +14018,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. - 2010-05-25T01:36:34Z + 2010-05-25T01:36:34Z neutrophillic cytoplasm @@ -14085,7 +14053,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -14121,7 +14089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -14156,7 +14124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -14174,7 +14142,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Heterochromatin that is arranged in a carthwheel pattern. - 2009-12-28T04:28:35Z + 2009-12-28T04:28:35Z cartwheel heterochromatin @@ -14258,8 +14226,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. - - 2014-02-11T17:29:04Z + + 2014-02-11T17:29:04Z CL:2000001 peripheral blood mononuclear cell @@ -14355,7 +14323,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 - Reactome:69278 @@ -17325,7 +17292,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. GOC:bf Wikipedia:GPCR - http://www.iuphar-db.org @@ -17458,32 +17424,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -18407,7 +18373,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0016194 GO:0016195 Wikipedia:Exocytosis @@ -18421,7 +18387,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GOC:mah ISBN:0716731363 PMID:22323285 @@ -19662,7 +19628,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -21234,7 +21199,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -21286,7 +21251,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:18391171 @@ -21321,7 +21286,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -23996,7 +23960,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -24561,6 +24525,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite primary metabolism biological_process GO:0044238 @@ -24576,7 +24541,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators - http://www.metacyc.org @@ -27603,31 +27567,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism - biological_process - GO:0071704 - - organic substance metabolic process - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - GOC:mah - - - - @@ -29157,63 +29096,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -31497,6 +31379,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -34411,6 +34301,39 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -34616,6 +34539,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -35469,7 +35444,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35505,14 +35480,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -35828,15 +35803,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -35873,34 +35848,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -36985,7 +36960,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37027,14 +37002,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -37454,7 +37429,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -37489,14 +37464,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -37536,7 +37511,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -37571,14 +37546,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -37619,7 +37594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -37660,14 +37635,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -37841,7 +37816,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37913,14 +37888,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -38323,7 +38298,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38373,14 +38348,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -38446,7 +38421,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -38491,7 +38466,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -38505,7 +38480,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -38893,7 +38868,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Skeletal element that is composed of bone tissue. @@ -38935,14 +38910,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -39008,7 +38983,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -39045,14 +39020,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -39279,8 +39254,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -39293,7 +39268,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39347,34 +39322,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -40208,9 +40183,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40258,15 +40233,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -40285,19 +40260,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -40337,8 +40312,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -40376,11 +40351,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -40393,13 +40368,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -40461,22 +40436,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -40509,45 +40484,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -40688,7 +40663,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40744,14 +40719,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -40963,7 +40938,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41016,14 +40991,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -41336,7 +41311,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -41359,14 +41334,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -41520,9 +41495,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -41551,34 +41526,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -41618,7 +41593,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -41644,7 +41619,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41657,7 +41632,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -41704,7 +41679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41744,7 +41719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41757,7 +41732,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -41807,15 +41782,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -41832,15 +41807,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -41853,19 +41828,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -41894,8 +41869,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -41919,11 +41894,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -41942,13 +41917,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -42167,7 +42142,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -42182,14 +42157,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -42484,8 +42459,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -42497,24 +42472,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -42567,7 +42542,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -42586,14 +42561,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -43217,7 +43192,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -43231,14 +43206,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -43265,7 +43240,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43304,14 +43279,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -44025,7 +44000,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44041,14 +44016,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -44165,7 +44140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44183,14 +44158,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -44356,7 +44331,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44366,7 +44341,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -44385,7 +44360,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -44479,7 +44454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44493,7 +44468,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -44506,7 +44481,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -44534,7 +44509,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44551,14 +44526,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45447,7 +45422,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45473,7 +45448,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -45489,7 +45464,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -45565,7 +45540,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -45573,7 +45548,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -45586,7 +45561,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -45689,7 +45664,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -45706,14 +45681,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -45741,7 +45716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45758,14 +45733,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45821,7 +45796,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45829,14 +45804,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45859,7 +45834,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45869,14 +45844,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -46015,7 +45990,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46035,14 +46010,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010210 blood clot - + - + BTO @@ -46163,8 +46138,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46176,11 +46151,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -46193,13 +46168,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46260,7 +46235,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46270,7 +46245,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46283,7 +46258,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46556,7 +46531,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46577,7 +46552,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -46590,7 +46565,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -47141,7 +47116,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47164,7 +47139,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47177,7 +47152,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47701,5 +47676,5 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.tsv b/src/ontology/subsets/blood_and_immune_upper_slim.tsv index 42e83f39e..a99388ad7 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.tsv +++ 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+_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid588 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid595 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid608 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid618 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid653 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid667 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid683 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid70 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid73 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid736 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid754 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid775 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid790 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid845 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid877 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid922 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid936 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid951 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid968 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid986 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid994 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -504,7 +503,6 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "hematopoietic lineage restricted progenitor cell" "hematopoietic oligopotent progenitor cell" "ecto-epithelial cell" - "meso-epithelial cell" "nongranular leukocyte" "bone marrow cell" "endothelial cell of vascular tree" @@ -908,7 +906,6 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "exocytic vesicle" "cellular response to chemical stimulus" "organelle assembly" - "organic substance metabolic process" "immunoglobulin heavy chain V-D-J recombination" "immunoglobulin light chain V-J recombination" "IgD immunoglobulin complex" @@ -952,7 +949,6 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "extracellular vesicle biogenesis" "export from cell" "defense response to symbiont" - "organic substance biosynthetic process" "regulation of leukocyte differentiation" "mitotic cell cycle process" "mononuclear cell differentiation" @@ -1125,11 +1121,13 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" "transmembrane emp24 domain-containing protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "G-protein coupled receptor" "eukaryotic protein" "cathepsin-like protease" + "protein-containing molecular entity" "processual entity" "tube" "vessel" diff --git a/src/ontology/subsets/eye_upper_slim.json b/src/ontology/subsets/eye_upper_slim.json index 8ad22264c..c7df74eb0 100644 --- a/src/ontology/subsets/eye_upper_slim.json +++ b/src/ontology/subsets/eye_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/eye_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -657,10 +504,6 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cuboidal endothelial cell of vascular tree" - } ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -3364,7 +3207,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://www.wikidata.org/entity/Q35563349" + "val" : "http://www.wikidata.org/entity/Q35563349" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-06-25T01:17:43Z" @@ -3393,30 +3236,6 @@ "val" : "https://orcid.org/0000-0002-0819-0473" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_4033015", "lbl" : "retinal astrocyte", @@ -3442,38 +3261,6 @@ "val" : "2023-03-02T14:38:32Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -3481,7 +3268,7 @@ "meta" : { "definition" : { "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", - "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + "xrefs" : [ "GOC:mah", "ISBN:0815316194" ] }, "comments" : [ "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -6343,7 +6130,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -6373,7 +6160,7 @@ "meta" : { "definition" : { "val" : "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:18391171" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6395,7 +6182,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -7287,7 +7074,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -7312,7 +7099,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:3077060" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { @@ -7795,13 +7582,16 @@ "meta" : { "definition" : { "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", - "xrefs" : [ "GOC:go_curators", "http://www.metacyc.org" ] + "xrefs" : [ "GOC:go_curators" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "primary metabolism" } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" @@ -8647,7 +8437,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.", + "val" : "Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.", "xrefs" : [ "GOC:ai", "GOC:dos", "GOC:dph", "GOC:tb" ] }, "synonyms" : [ { @@ -9100,40 +8890,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071704", - "lbl" : "organic substance metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance metabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-03-08T03:32:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0071826", "lbl" : "protein-RNA complex organization", @@ -9896,62 +9652,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1903047", "lbl" : "mitotic cell cycle process", @@ -10069,260 +9769,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], - "xrefs" : [ { - "val" : "IAO:0000233" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." - }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -10991,73 +10437,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -13132,6 +12511,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -13187,3109 +12590,6558 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000053" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000019", + "lbl" : "camera-type eye", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + "val" : "An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.", + "xrefs" : [ "GO:0043010", "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "eye", + "xrefs" : [ "FMA:54448" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio orbitalis", + "xrefs" : [ "FMA:54448", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "vertebrate eye" + }, { + "pred" : "hasRelatedSynonym", + "val" : "camera-type eye plus associated structures" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "eyes", + "xrefs" : [ "TAO:0000107" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "orbital part of face", + "xrefs" : [ "FMA:54448" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "orbital region", + "xrefs" : [ "FMA:54448" ] + } ], "xrefs" : [ { - "val" : "RO:0000056" + "val" : "AAO:0010340" + }, { + "val" : "BIRNLEX:1169" + }, { + "val" : "BTO:0004688" + }, { + "val" : "EHDAA2:0000484" + }, { + "val" : "EHDAA:936" + }, { + "val" : "EMAPA:16198" + }, { + "val" : "FMA:54448" + }, { + "val" : "MA:0000261" + }, { + "val" : "NCIT:C12401" + }, { + "val" : "SCTID:181143004" + }, { + "val" : "TAO:0000107" + }, { + "val" : "UMLS:C0015392" + }, { + "val" : "UMLS:C1280202" + }, { + "val" : "VHOG:0000275" + }, { + "val" : "XAO:0000179" + }, { + "val" : "ZFA:0000107" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000020", + "lbl" : "sense organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "An organ that is capable of transducing sensory stimulus to the nervous system.", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/549", "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "organ of sense organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory system organ", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "sensillum", + "xrefs" : [ "WBbt:0006929" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Sinnesorgan", + "xrefs" : [ "BTO:0000202" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "sensor" + } ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "AEO:0000094" + }, { + "val" : "BSA:0000121" + }, { + "val" : "BTO:0000202" + }, { + "val" : "CALOHA:TS-2043" + }, { + "val" : "EHDAA2:0001824" + }, { + "val" : "EHDAA:500" + }, { + "val" : "EMAPA:35955" + }, { + "val" : "FBbt:00005155" + }, { + "val" : "GAID:63" + }, { + "val" : "HAO:0000930" + }, { + "val" : "MA:0000017" + }, { + "val" : "MESH:D012679" + }, { + "val" : "NCIT:C33224" + }, { + "val" : "SCTID:244485009" + }, { + "val" : "UMLS:C0935626" + }, { + "val" : "VHOG:0001407" + }, { + "val" : "WBbt:0006929" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], + "xrefs" : [ { + "val" : "galen:Tube" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000033", + "lbl" : "head", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "The head is the anterior-most division of the body [GO].", + "xrefs" : [ "GO:0060322", "Wikipedia:Head" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "head (volume)", + "xrefs" : [ "FMA:7154" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult head" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cephalic area", + "xrefs" : [ "SPD:0000016" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010335" + }, { + "val" : "AEO:0000106" + }, { + "val" : "BILA:0000115" + }, { + "val" : "BIRNLEX:1230" + }, { + "val" : "BTO:0000282" + }, { + "val" : "CALOHA:TS-0436" + }, { + "val" : "EFO:0000964" + }, { + "val" : "EHDAA2:0003106" + }, { + "val" : "EMAPA:31858" + }, { + "val" : "FMA:7154" + }, { + "val" : "GAID:61" + }, { + "val" : "HAO:0000397" + }, { + "val" : "MA:0000023" + }, { + "val" : "MAT:0000294" + }, { + "val" : "MESH:D006257" + }, { + "val" : "MIAA:0000294" + }, { + "val" : "NCIT:C12419" + }, { + "val" : "SCTID:302548004" + }, { + "val" : "SPD:0000016" + }, { + "val" : "TAO:0001114" + }, { + "val" : "TGMA:0000002" + }, { + "val" : "UMLS:C0018670" + }, { + "val" : "VHOG:0001644" + }, { + "val" : "WBbt:0005739" + }, { + "val" : "Wikipedia:Head" + }, { + "val" : "XAO:0003024" + }, { + "val" : "ZFA:0001114" + }, { + "val" : "galen:Head" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000042", + "lbl" : "serous membrane", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.", + "xrefs" : [ "Wikipedia:Serous_membrane", "https://github.com/obophenotype/uberon/issues/86" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "tunica serosa", + "xrefs" : [ "FMA:9581" ] + }, { + "pred" : "hasExactSynonym", + "val" : "wall of serous sac", + "xrefs" : [ "FMA:9581" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "serosa", + "xrefs" : [ "Wikipedia:Serous_membrane" ] + } ], + "xrefs" : [ { + "val" : "FMA:9581" + }, { + "val" : "GAID:19" + }, { + "val" : "MESH:D012704" + }, { + "val" : "NCIT:C13169" + }, { + "val" : "SCTID:362878009" + }, { + "val" : "TAO:0005425" + }, { + "val" : "UMLS:C0036760" + }, { + "val" : "Wikipedia:Serous_membrane" + }, { + "val" : "ZFA:0005425" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000047", + "lbl" : "simple eye", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.", + "xrefs" : [ "Wikipedia:Eye#Simple_eyes" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "TGMA:0000729" + }, { + "val" : "Wikipedia:Eye#Simple_eyes" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000055", + "lbl" : "vessel", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "A tubular structure that contains, conveys body fluid, such as blood or lymph.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. 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The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.", + "xrefs" : [ "GO:0007369" ] }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blastocystis trilaminaris stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000109" + }, { + "val" : "BilaDO:0000008" + }, { + "val" : "EFO:0001296" + }, { + "val" : "FBdv:00005317" + }, { + "val" : "HsapDv:0000010" + }, { + "val" : "MmusDv:0000013" + }, { + "val" : "OGES:000004" + }, { + "val" : "OGES:000019" + }, { + "val" : "WBls:0000010" + }, { + "val" : "XAO:1000005" + }, { + "val" : "ZFS:0000047" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000110", + "lbl" : "neurula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + "val" : "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.", + "xrefs" : [ "GO:0001841" ] }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BILS:0000110" + }, { + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000122", + "lbl" : "neuron projection bundle", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + "val" : "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.", + "xrefs" : [ "CARO:0001001", "FBC:DOS", "FBbt:00005099" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "funiculus" + }, { + "pred" : "hasExactSynonym", + "val" : "nerve fiber bundle", + "xrefs" : [ "FBbt:00005099" ] + }, { + "pred" : "hasExactSynonym", + "val" : "neural fiber bundle" + } ], + "xrefs" : [ { + "val" : "CARO:0001001" + }, { + "val" : "FBbt:00005099" + }, { + "val" : "NLX:147821" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0005163" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000153", + "lbl" : "anterior region of body", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" - }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000154", + "lbl" : "posterior region of body", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000165", + "lbl" : "mouth", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "xrefs" : [ "Wikipedia:Mouth", "https://github.com/obophenotype/uberon/wiki/The-digestive-tract" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio oralis", + "xrefs" : [ "BTO:0004698", "FMA:49184", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "cavital oralis", + "xrefs" : [ "Wikipedia:Mouth" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavitas oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavum oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth cavity", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral region", + "xrefs" : [ "EHDAA2:0001326" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral vestibule", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "rima oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "stoma" + }, { + "pred" : "hasRelatedSynonym", + "val" : "stomatodaeum", + "xrefs" : [ "VHOG:0000812" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trophic apparatus", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibule of mouth", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibulum oris", + "xrefs" : [ "BTO:0001090" ] + } ], "xrefs" : [ { - "val" : "RO:0002180" + "val" : "AAO:0010355" + }, { + "val" : "BTO:0001090" + }, { + "val" : "BTO:0004698" + }, { + "val" : "CALOHA:TS-1315" + }, { + "val" : "EFO:0000825" + }, { + "val" : "EHDAA2:0001326" + }, { + "val" : "EHDAA:542" + }, { + "val" : "EMAPA:16262" + }, { + "val" : "FBbt:00003126" + }, { + "val" : "FMA:49184" + }, { + "val" : "GAID:75" + }, { + "val" : "MA:0000341" + }, { + "val" : "MA:0002474" + }, { + "val" : "MAT:0000038" + }, { + "val" : "MESH:D009055" + }, { + "val" : "MIAA:0000038" + }, { + "val" : "SCTID:21082005" + }, { + "val" : "TADS:0000040" + }, { + "val" : "TAO:0000547" + }, { + "val" : "TAO:0000590" + }, { + "val" : "TGMA:0000131" + }, { + "val" : "VHOG:0000280" + }, { + "val" : "VHOG:0000812" + }, { + "val" : "Wikipedia:Mouth" + }, { + "val" : "XAO:0003029" + }, { + "val" : "ZFA:0000547" + }, { + "val" : "ZFA:0000590" + }, { + "val" : "galen:Mouth" + }, { + "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "val" : "https://github.com/obophenotype/uberon/issues/661" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "lbl" : "blood", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + "val" : "A fluid that is composed of blood plasma and erythrocytes.", + "xrefs" : [ "FMA:9670", "Wikipedia:Blood", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/9" ] }, - "comments" : [ "TODO - add child relations from DOS" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "portion of blood" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "pred" : "hasExactSynonym", + "val" : "vertebrate blood" + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole blood", + "xrefs" : [ "BTO:0000089" ] + } ], "xrefs" : [ { - "val" : "RO:0002212" + "val" : "AAO:0000046" + }, { + "val" : "BTO:0000089" + }, { + "val" : "CALOHA:TS-0079" + }, { + "val" : "EFO:0000296" + }, { + "val" : "EHDAA2:0000176" + }, { + "val" : "EHDAA:418" + }, { + "val" : "EMAPA:16332" + }, { + "val" : "ENVO:02000027" + }, { + "val" : "EV:0100047" + }, { + "val" : "FMA:9670" + }, { + "val" : "GAID:965" + }, { + "val" : "MA:0000059" + }, { + "val" : "MESH:D001769" + }, { + "val" : "MIAA:0000315" + }, { + "val" : "NCIT:C12434" + }, { + "val" : "TAO:0000007" + }, { + "val" : "UMLS:C0005767" + }, { + "val" : "VHOG:0000224" + }, { + "val" : "Wikipedia:Blood" + }, { + "val" : "XAO:0000124" + }, { + "val" : "ZFA:0000007" + }, { + "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "negatively_regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000179", + "lbl" : "haemolymphatic fluid", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + "val" : "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blood or blood analog" + }, { + "pred" : "hasRelatedSynonym", + "val" : "circulating fluid" + } ], "xrefs" : [ { - "val" : "RO:0002213" + "val" : "CARO:0000081" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "positively_regulates" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-04-08T04:38:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", + "lbl" : "blastula", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blastula embryo", + "xrefs" : [ "BILA:0000059" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastosphere", + "xrefs" : [ "Wikipedia:Blastula" ] + } ], "xrefs" : [ { - "val" : "RO:0002215" + "val" : "BILA:0000059" + }, { + "val" : "BTO:0000128" + }, { + "val" : "GAID:1294" + }, { + "val" : "MESH:D036703" + }, { + "val" : "OGEM:000006" + }, { + "val" : "Wikipedia:Blastula" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007011" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable of part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", + "lbl" : "musculature of body", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", + "xrefs" : [ "VSAO:0000033" ] }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "muscle system" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" + "pred" : "hasExactSynonym", + "val" : "muscle system of body" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002219", - "lbl" : "surrounded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002220", - "lbl" : "adjacent to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x adjacent to y if and only if x and y share a boundary." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "pred" : "hasExactSynonym", + "val" : "muscular system", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "musculature system", + "xrefs" : [ "BILA:0000088" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of all muscles", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of muscles of body", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate muscular system", + "xrefs" : [ "BTO:0001369" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "muskelsystem", + "xrefs" : [ "BTO:0001485" ] + } ], "xrefs" : [ { - "val" : "RO:0002220" + "val" : "AAO:0000307" + }, { + "val" : "BILA:0000088" + }, { + "val" : "BTO:0001369" + }, { + "val" : "BTO:0001485" + }, { + "val" : "EFO:0000801" + }, { + "val" : "FMA:72954" + }, { + "val" : "MA:0002888" + }, { + "val" : "MAT:0000025" + }, { + "val" : "MIAA:0000025" + }, { + "val" : "VSAO:0000033" + }, { + "val" : "XAO:0004042" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation acts as a join point with BSPO" + "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "adjacent_to" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002221", - "lbl" : "surrounds", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", + "lbl" : "organism substance", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of surrounded by" + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002223", - "lbl" : "starts", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of starts with" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002224", - "lbl" : "starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "body fluid or substance", + "xrefs" : [ "MA:0002450" ] + }, { + "pred" : "hasExactSynonym", + "val" : "body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organism substance", + "xrefs" : [ "CARO:0000004" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance", + "xrefs" : [ "ZFA:0001487" ] + } ], "xrefs" : [ { - "val" : "RO:0002224" + "val" : "AAO:0010839" + }, { + "val" : "AEO:0000004" + }, { + "val" : "BILA:0000004" + }, { + "val" : "CALOHA:TS-2101" + }, { + "val" : "CARO:0000004" + }, { + "val" : "EHDAA2:0003004" + }, { + "val" : "EMAPA:35178" + }, { + "val" : "FBbt:00007019" + }, { + "val" : "FMA:9669" + }, { + "val" : "HAO:0000004" + }, { + "val" : "MA:0002450" + }, { + "val" : "NCIT:C13236" + }, { + "val" : "SPD:0000008" + }, { + "val" : "TAO:0001487" + }, { + "val" : "TGMA:0001824" + }, { + "val" : "VHOG:0001726" + }, { + "val" : "XAO:0004001" + }, { + "val" : "ZFA:0001487" + }, { + "val" : "galen:BodySubstance" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts_with" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002225", - "lbl" : "develops from part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002226", - "lbl" : "develops in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops_in y if x is located in y whilst x is developing" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", - "lbl" : "ends", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of ends with" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", - "lbl" : "ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000464", + "lbl" : "anatomical space", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "lumen" + }, { + "pred" : "hasBroadSynonym", + "val" : "space" + }, { + "pred" : "hasExactSynonym", + "val" : "lumen space" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "anatomical spaces", + "xrefs" : [ "ZFA:0001643" ] + } ], "xrefs" : [ { - 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Consider merging with 'neuron projection bundle'" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "fascicle", + "xrefs" : [ "FBbt:00005101" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "fasciculus" + }, { + "pred" : "hasExactSynonym", + "val" : "nerve bundle", + "xrefs" : [ "FMA:12235" ] + }, { + "pred" : "hasExactSynonym", + "val" : "nerve fasciculus", + "xrefs" : [ "FMA:12235" ] + }, { + "pred" : "hasExactSynonym", + "val" : "neural fasciculus", + "xrefs" : [ "FMA:12235" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "nerve fiber tract", + "xrefs" : [ "BTO:0002191" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:872" + }, { + "val" : "BTO:0002191" + }, { + "val" : "EMAPA:36605" + }, { + "val" : "FMA:12235" + }, { + "val" : "NCIT:C32586" + }, { + "val" : "TGMA:0000088" + }, { + "val" : "UMLS:C1185741" + }, { + "val" : "Wikipedia:Nervous_system_fascicle" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", - "lbl" : "causally downstream of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001032", + "lbl" : "sensory system", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of upstream of" + "val" : "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.", + "xrefs" : [ "Wikipedia:Sensory_system" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "organa sensuum", + "xrefs" : [ "FMA:75259", "FMA:TA" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organ subsystem" + }, { + "pred" : "hasExactSynonym", + "val" : "sense organs", + "xrefs" : [ "FMA:75259" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organs set", + "xrefs" : [ "FMA:75259" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory subsystem" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "sensory systems", + "xrefs" : [ "TAO:0000282" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "organa sensuum", + "xrefs" : [ "Wikipedia:Sensory_system" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "sensory organ system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of sense organs", + "xrefs" : [ "FMA:75259" ] + } ], "xrefs" : [ { - "val" : "RO:0002404" + "val" : "AAO:0000555" + }, { + "val" : "BAMS:SEN" + }, { + "val" : "BILA:0000099" + }, { + "val" : "EFO:0000805" + }, { + "val" : "EHDAA2:0003094" + }, { + "val" : "EMAPA:16192" + }, { + "val" : "FBbt:00007692" + }, { + "val" : "FMA:75259" + }, { + "val" : "MA:0002442" + }, { + "val" : "MAT:0000031" + }, { + "val" : "MIAA:0000031" + }, { + "val" : "NLXANAT:090816" + }, { + "val" : "TAO:0000282" + }, { + "val" : "VHOG:0001674" + }, { + "val" : "Wikipedia:Sensory_system" + }, { + "val" : "XAO:0003194" + }, { + "val" : "ZFA:0000282" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_downstream_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", - "lbl" : "causally related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This branch of the ontology deals with causal relations between entities. 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001048", + "lbl" : "primordium", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + "val" : "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. 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The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].", + "xrefs" : [ "Wikipedia:Neural_tube" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "affects" + "val" : "neural primordium" + }, { + "pred" : "hasRelatedSynonym", + "val" : "presumptive central nervous system" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tubus neuralis", + "xrefs" : [ "Wikipedia:Neural_tube" ] } ], "xrefs" : [ { - "val" : "RO:0002418" + "val" : "AAO:0010617" + }, { + "val" : "BTO:0001057" + }, { + "val" : "CALOHA:TS-2371" + }, { + "val" : "DHBA:10154" + }, { + "val" : "EHDAA2:0001254" + }, { + "val" : "EHDAA:2869" + }, { + "val" : "EHDAA:908" + }, { + "val" : "EMAPA:16164" + }, { + "val" : "EMAPA:16757" + }, { + "val" : "FMA:293882" + }, { + "val" : "MAT:0000069" + }, { + "val" : "MIAA:0000069" + }, { + "val" : "NCIT:C34226" + }, { + "val" : "SCTID:362852000" + }, { + "val" : "TAO:0001135" + }, { + "val" : "UMLS:C0231024" + }, { + "val" : "VHOG:0000307" + }, { + "val" : "Wikipedia:Neural_tube" + }, { + "val" : "XAO:0003204" + }, { + "val" : "ZFA:0001135" + }, { + "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_upstream_of_or_within" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002427", - "lbl" : "causally downstream of or within", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "lbl" : "anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of causally upstream of or within" + "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", + "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002427" + "val" : "AAO:0010841" + }, { + "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" + }, { + "val" : "BILA:0000000" + }, { + "val" : "BIRNLEX:6" + }, { + "val" : "CARO:0000000" + }, { + "val" : "EHDAA2:0002229" + }, { + "val" : "FBbt:10000000" + }, { + "val" : "FMA:62955" + }, { + "val" : "HAO:0000000" + }, { + "val" : "MA:0000001" + }, { + "val" : "NCIT:C12219" + }, { + "val" : "TAO:0100000" + }, { + "val" : "TGMA:0001822" + }, { + "val" : "UMLS:C1515976" + }, { + "val" : "WBbt:0000100" + }, { + "val" : "XAO:0000000" + }, { + "val" : "ZFA:0100000" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_downstream_of_or_within" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", - "lbl" : "involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", - "lbl" : "involved in or involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", - "lbl" : "contributes to morphology of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", - "lbl" : "composed primarily of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", - "lbl" : "has part that occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "lbl" : "receives input from", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "lbl" : "sends output to", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", - "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", - "lbl" : "existence starts during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. 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The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "exists during" + "val" : "involuntary muscle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-striated muscle" + }, { + "pred" : "hasExactSynonym", + "val" : "smooth muscle" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "textus muscularis nonstriatus", + "xrefs" : [ "FMA:14070", "FMA:TA" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasNarrowSynonym", + "val" : "visceral muscle" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasNarrowSynonym", + "val" : "visceral muscle tissue" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "textus muscularis levis; textus muscularis nonstriatus", + "xrefs" : [ "Wikipedia:Smooth_muscle_tissue" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010244" + }, { + "val" : "AEO:0000141" + }, { + "val" : "BTO:0001260" + }, { + "val" : "CALOHA:TS-0943" + }, { + "val" : "EFO:0000889" + }, { + "val" : "EHDAA2:0003141" + }, { + "val" : "EMAPA:32717" + }, { + "val" : "EV:0100378" + }, { + "val" : "FMA:14070" + }, { + "val" : "GAID:167" + }, { + "val" : "MA:0000166" + }, { + "val" : "MAT:0000303" + }, { + "val" : "MESH:D009130" + }, { + "val" : "MIAA:0000303" + }, { + "val" : "NCIT:C12437" + }, { + "val" : "TAO:0005274" + }, { + "val" : "UMLS:C1267092" + }, { + "val" : "VHOG:0001246" + }, { + "val" : "WBbt:0005781" + }, { + "val" : "Wikipedia:Smooth_muscle_tissue" + }, { + "val" : "XAO:0000175" + }, { + "val" : "ZFA:0005274" + }, { + "val" : "galen:SmoothMuscle" + }, { + "val" : "galen:SmoothMuscleTissue" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", - "lbl" : "existence ends during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. 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The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].", + "xrefs" : [ "FMA:62004", "GO:0021550", "Wikipedia:Bone_marrow_of_ovary_oblongata" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of blood" + "pred" : "hasBroadSynonym", + "val" : "bulb" + }, { + "pred" : "hasBroadSynonym", + "val" : "medulla", + "xrefs" : [ "ABA:MY" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "vertebrate blood" + "val" : "bulbus", + "xrefs" : [ "FMA:62004", "FMA:TA" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "whole blood", - "xrefs" : [ "BTO:0000089" ] + "val" : "medulla oblonzata", + "xrefs" : [ "Wikipedia:Medulla_oblongata" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metepencephalon", + "xrefs" : [ "FMA:62004" ] } ], "xrefs" : [ { - "val" : "AAO:0000046" + "val" : "AAO:0010486" }, { - "val" : "BTO:0000089" + "val" : "BAMS:MY" }, { - "val" : "CALOHA:TS-0079" + "val" : "BAMS:Md" }, { - "val" : "EFO:0000296" + "val" : "BIRNLEX:957" }, { - "val" : "EHDAA2:0000176" + "val" : "BM:Me" }, { - "val" : "EHDAA:418" + "val" : "BTO:0000041" }, { - "val" : "EMAPA:16332" + "val" : "CALOHA:TS-0607" }, { - "val" : "ENVO:02000027" + "val" : "DMBA:17352" }, { - "val" : "EV:0100047" + "val" : "EFO:0000924" }, { - "val" : "FMA:9670" + "val" : "EHDAA2:0001088" }, { - "val" : "GAID:965" + "val" : "EHDAA:7588" }, { - "val" : "MA:0000059" + "val" : "EMAPA:17550" }, { - "val" : "MESH:D001769" + "val" : "EV:0100275" }, { - "val" : "MIAA:0000315" + "val" : "FMA:62004" }, { - "val" : "NCIT:C12434" + "val" : "GAID:590" }, { - "val" : "TAO:0000007" + "val" : "MA:0000206" }, { - "val" : "UMLS:C0005767" + "val" : "MAT:0000111" }, { - "val" : "VHOG:0000224" + "val" : "MAT:0000367" }, { - "val" : "Wikipedia:Blood" + "val" : "MBA:354" }, { - "val" : "XAO:0000124" + "val" : "MESH:D008526" }, { - "val" : "ZFA:0000007" + "val" : "MIAA:0000111" }, { - "val" : "galen:Blood" + "val" : "NCIT:C12442" + }, { + "val" : "SCTID:279104005" + }, { + "val" : "TAO:0000545" + }, { + "val" : "UMLS:C0025148" + }, { + "val" : "UMLS:C1269575" + }, { + "val" : "VHOG:0000181" + }, { + "val" : "Wikipedia:Bone_marrow_of_ovary_oblongata" + }, { + "val" : "XAO:0003100" + }, { + "val" : "ZFA:0000545" + }, { + "val" : "neuronames:698" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -17594,3235 +20575,3334 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "lbl" : "haemolymphatic fluid", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001908", + "lbl" : "optic tract", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF].", + "xrefs" : [ "NIFSTD", "Wikipedia:Optic_tract", "ZFIN:curator" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "blood or blood analog" + "pred" : "hasExactSynonym", + "val" : "optic lemniscus" }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "circulating fluid" - } ], - "xrefs" : [ { - "val" : "CARO:0000081" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "optic tracts", + "xrefs" : [ "ZFA:0000252" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-04-08T04:38:19Z" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tractus optici", + "xrefs" : [ "NeuroNames:460" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", - "lbl" : "blastula", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", - "xrefs" : [ "Wikipedia:Blastula" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blastula embryo", - "xrefs" : [ "BILA:0000059" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tractus opticus", + "xrefs" : [ "Wikipedia:Optic_tract" ] }, { "pred" : "hasRelatedSynonym", - "val" : "blastosphere", - "xrefs" : [ "Wikipedia:Blastula" ] + "val" : "visual pathway", + "xrefs" : [ "GAID:735" ] } ], "xrefs" : [ { - "val" : "BILA:0000059" + "val" : "BAMS:opt" }, { - "val" : "BTO:0000128" + "val" : "BIRNLEX:1684" }, { - "val" : "GAID:1294" + "val" : "BM:Tel-OT" }, { - "val" : "MESH:D036703" + "val" : "DHBA:10589" }, { - "val" : "OGEM:000006" + "val" : "DMBA:17785" }, { - "val" : "Wikipedia:Blastula" + "val" : "EMAPA:35617" + }, { + "val" : "FMA:62046" + }, { + "val" : "GAID:735" + }, { + "val" : "HBA:9309" + }, { + "val" : "MA:0001099" + }, { + "val" : "MBA:125" + }, { + "val" : "MESH:D014795" + }, { + "val" : "NCIT:C33218" + }, { + "val" : "SCTID:280952003" + }, { + "val" : "TAO:0000252" + }, { + "val" : "UMLS:C0152405" + }, { + "val" : "VHOG:0001164" + }, { + "val" : "Wikipedia:Optic_tract" + }, { + "val" : "XAO:0004101" + }, { + "val" : "ZFA:0000252" + }, { + "val" : "neuronames:460" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" + "val" : "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "lbl" : "musculature of body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001943", + "lbl" : "midbrain tegmentum", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", - "xrefs" : [ "VSAO:0000033" ] + "val" : "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].", + "xrefs" : [ "FMA:FMA", "ISBN:0471888893", "Wikipedia:Midbrain_tegmentum" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "muscle system" - }, { - "pred" : "hasExactSynonym", - "val" : "muscle system of body" - }, { - "pred" : "hasExactSynonym", - "val" : "muscular system", - "xrefs" : [ "FMA:72954" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasBroadSynonym", + "val" : "MTg", + "xrefs" : [ "BIRNLEX:1200", "NIFSTD:NeuroNames_abbrevSource" ] }, { - "pred" : "hasExactSynonym", - "val" : "musculature system", - "xrefs" : [ "BILA:0000088" ] + "pred" : "hasBroadSynonym", + "val" : "tegmentum", + "xrefs" : [ "ISBN:0471888893" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "set of all muscles", - "xrefs" : [ "FMA:72954" ] + "val" : "tegmentum mesencephali", + "xrefs" : [ "Wikipedia:Midbrain_tegmentum" ] }, { "pred" : "hasExactSynonym", - "val" : "set of muscles of body", - "xrefs" : [ "FMA:72954" ] + "val" : "tegmentum of midbrain" }, { - "pred" : "hasExactSynonym", - "val" : "vertebrate muscular system", - "xrefs" : [ "BTO:0001369" ] + "pred" : "hasRelatedSynonym", + "val" : "mesencephalic tegmentum", + "xrefs" : [ "VHOG:0001367" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "muskelsystem", - "xrefs" : [ "BTO:0001485" ] + "val" : "tegmentum mesencephalicum", + "xrefs" : [ "NeuroNames:491" ] } ], "xrefs" : [ { - "val" : "AAO:0000307" + "val" : "BAMS:MTg" }, { - "val" : "BILA:0000088" + "val" : "BIRNLEX:1200" }, { - "val" : "BTO:0001369" + "val" : "BTO:0003388" }, { - "val" : "BTO:0001485" + "val" : "DHBA:12195" + }, { + "val" : "EFO:0000921" + }, { + "val" : "EHDAA2:0004475" + }, { + "val" : "EMAPA:18215" + }, { + "val" : "FMA:62393" + }, { + "val" : "HBA:9002" + }, { + "val" : "MA:0000212" + }, { + "val" : "MAT:0000452" + }, { + "val" : "SCTID:362392007" }, { - "val" : "EFO:0000801" + "val" : "TAO:0000160" }, { - "val" : "FMA:72954" + "val" : "UMLS:C0039441" }, { - "val" : "MA:0002888" + "val" : "VHOG:0001367" }, { - "val" : "MAT:0000025" + "val" : "Wikipedia:Midbrain_tegmentum" }, { - "val" : "MIAA:0000025" + "val" : "XAO:0004271" }, { - "val" : "VSAO:0000033" + "val" : "ZFA:0000160" }, { - "val" : "XAO:0004042" + "val" : "neuronames:491" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "lbl" : "blood plasma", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "The liquid component of blood, in which erythrocytes are suspended.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "body fluid or substance", - "xrefs" : [ "MA:0002450" ] - }, { - "pred" : "hasExactSynonym", - "val" : "body substance", - "xrefs" : [ "FMA:9669" ] + "pred" : "hasBroadSynonym", + "val" : "plasma", + "xrefs" : [ "MA:0002501" ] }, { - "pred" : "hasExactSynonym", - "val" : "organism substance", - "xrefs" : [ "CARO:0000004" ] + "pred" : "hasBroadSynonym", + "val" : "portion of plasma", + "xrefs" : [ "FMA:62970" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of body substance", - "xrefs" : [ "FMA:9669" ] + "val" : "blood plasm" }, { "pred" : "hasExactSynonym", - "val" : "portion of organism substance", - "xrefs" : [ "ZFA:0001487" ] + "val" : "portion of blood plasma" } ], "xrefs" : [ { - "val" : "AAO:0010839" - }, { - "val" : "AEO:0000004" - }, { - "val" : "BILA:0000004" - }, { - "val" : "CALOHA:TS-2101" - }, { - "val" : "CARO:0000004" - }, { - "val" : "EHDAA2:0003004" - }, { - "val" : "EMAPA:35178" + "val" : "BTO:0000131" }, { - "val" : "FBbt:00007019" + "val" : "CALOHA:TS-0800" }, { - "val" : "FMA:9669" + "val" : "EFO:0001905" }, { - "val" : "HAO:0000004" + "val" : "EMAPA:35690" }, { - "val" : "MA:0002450" + "val" : "FMA:62970" }, { - "val" : "NCIT:C13236" + "val" : "GAID:1178" }, { - "val" : "SPD:0000008" + "val" : "MA:0002501" }, { - "val" : "TAO:0001487" + "val" : "MAT:0000052" }, { - "val" : "TGMA:0001824" + "val" : "MESH:D010949" }, { - "val" : "VHOG:0001726" + "val" : "MIAA:0000052" }, { - "val" : "XAO:0004001" + "val" : "NCIT:C13356" }, { - 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it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.", + "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "visceral organ", + "xrefs" : [ "RETIRED_EHDAA2:0002201" ] + }, { + "pred" : "hasExactSynonym", + "val" : "visceral organ system", + "xrefs" : [ "MA:0000019" ] + }, { "pred" : "hasRelatedSynonym", - "val" : "acellular anatomical structures", - "xrefs" : [ "ZFA:0000382" ] + "val" : "splanchnic tissue", + "xrefs" : [ "BTO:0001491" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "viscera" + }, { + "pred" : "hasRelatedSynonym", + "val" : "visceral tissue", + "xrefs" : [ "BTO:0001491" ] } ], "xrefs" : [ { - "val" : "AAO:0010268" + "val" : "AAO:0010386" }, { - "val" : "AEO:0000040" + "val" : "BTO:0001491" }, { - "val" : "BILA:0000040" + "val" : "EHDAA:512" }, { - "val" : "CARO:0000040" + "val" : "EMAPA:16245" }, { - "val" : "EHDAA2:0003040" + "val" : "FMA:7085" }, { - "val" : "FBbt:00007013" + "val" : "MA:0000019" }, { - "val" : "FMA:63863" + "val" : "MESH:D014781" }, { - "val" : "HAO:0000040" + "val" : "NCIT:C28287" }, { - "val" : "TAO:0000382" + "val" : "RETIRED_EHDAA2:0002201" }, { - "val" : "TGMA:0001841" + "val" : "SCTID:118760003" }, { - "val" : "XAO:0003162" + "val" : "UMLS:C0042779" }, { - "val" : "ZFA:0000382" + "val" : "Wikipedia:Viscus" + }, { + "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", - "lbl" : "anatomical cluster", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", + "lbl" : "postcranial axial skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical group whose component anatomical structures lie in close proximity to each other.", - "xrefs" : [ "FBbt:00007277" ] + "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", + "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FBbt:00007277" + "comments" : [ "previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "axial skeleton", + "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] }, { - "val" : "VHOG:0001737" + "pred" : "hasExactSynonym", + "val" : "post-cranial axial skeleton" } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + "xrefs" : [ { + "val" : "AAO:0000034" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "val" : "EFO:0000942" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "EHDAA2:0000161" + }, { + "val" : "EHDAA:5049" + }, { + "val" : "EMAPA:37721" + }, { + "val" : "FMA:71221" + }, { + "val" : "MA:0002986" + }, { + "val" : "MAT:0000148" + }, { + "val" : "MIAA:0000148" + }, { + "val" : "TAO:0000317" + }, { + "val" : "VHOG:0000317" + }, { + "val" : "VSAO:0000093" + }, { + "val" : "XAO:0003073" }, { + "val" : "ZFA:0000317" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", - "lbl" : "tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", + "lbl" : "trunk", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", - "xrefs" : [ "CARO:0000043" ] + "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. 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Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "embryonic tissue", - "xrefs" : [ "FMA:69069" ] + "pred" : "hasExactSynonym", + "val" : "CNS tract/commissure", + "xrefs" : [ "ZFA:0001682" ] }, { "pred" : "hasExactSynonym", - "val" : "germinal layer", - "xrefs" : [ "ncithesaurus:Germinal_Layer" ] + "val" : "neuronal white matter", + "xrefs" : [ "AEO:0001011" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "primary germ layer", - "xrefs" : [ "GO:0001704", "ZFA:0001122" ] + "pred" : "hasExactSynonym", + "val" : "white matter of neuraxis", + "xrefs" : [ "FMA:83929" ] + }, { + "pred" : "hasExactSynonym", + "val" : "white substance" }, { "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layer" + "val" : "CNS tracts and commissures", + "xrefs" : [ "TAO:0000145" ] }, { "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layers" + "val" : "CNS white matter", + "xrefs" : [ "TAO:0002143" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "substantia alba", + "xrefs" : [ "Wikipedia:White_matter" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "white mater", + "xrefs" : [ "VHOG:0001764" ] } ], "xrefs" : [ { - "val" : "AAO:0000480" + "val" : "AEO:0000139" }, { - "val" : "BILA:0000035" + "val" : "AEO:0001011" }, { - "val" : "BTO:0000556" + "val" : "EMAPA:35927" }, { - "val" : "EMAPA:36033" + "val" : "FMA:83929" }, { - "val" : "FBbt:00000110" + "val" : "HBA:9218" }, { - "val" : "FMA:69069" + "val" : "MA:0001135" }, { - "val" : "GAID:1303" + "val" : "NCIT:C33892" }, { - "val" : "MESH:D005855" + "val" : "NLX:412" }, { - "val" : "NCIT:C12950" + "val" : "NLXANAT:101177" }, { - "val" : "NCIT:C54105" + "val" : "PBA:294022044" }, { - "val" : "TAO:0001122" + "val" : "TAO:0000145" }, { - "val" : "UMLS:C0920502" + "val" : "TAO:0002142" }, { - "val" : "UMLS:C1708239" + "val" : "TAO:0002143" }, { - "val" : "VHOG:0001223" + "val" : "UMLS:C0682708" }, { - "val" : "Wikipedia:Germ_layer" + "val" : "VHOG:0001764" }, { - "val" : "XAO:0003011" + "val" : "Wikipedia:White_matter" }, { - "val" : "ZFA:0001122" + "val" : "ZFA:0001682" + }, { + "val" : "neuronames:2870" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", - "lbl" : "ectoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", + "lbl" : "coelemic cavity lumen", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", - "xrefs" : [ "Wikipedia:Ectoderm" ] + "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. 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In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "pred" : "hasExactSynonym", + "val" : "embryonic notocord" + }, { + "pred" : "hasExactSynonym", + "val" : "notocord", + "xrefs" : [ "ZFA:0000135" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "entoderm", - "xrefs" : [ "DOI:10.5962/bhl.title.1013" ] + "val" : "notochorda", + "xrefs" : [ "Wikipedia:Notochord" ] } ], "xrefs" : [ { - "val" : "AAO:0000139" + "val" : "AAO:0000327" }, { - "val" : "BILA:0000038" + "val" : "BTO:0001768" }, { - "val" : "BTO:0000800" + "val" : "CALOHA:TS-0690" }, { - "val" : "CALOHA:TS-0273" + "val" : "EHDAA2:0001277" }, { - "val" : "EFO:0002545" + "val" : "EHDAA:1241" }, { - "val" : "EHDAA2:0000436" + "val" : "EHDAA:6021" }, { - "val" : "EMAPA:16062" + "val" : "EMAPA:16191" }, { - "val" : "EV:0100005" + "val" : "EV:0100002" }, { - "val" : "FBbt:00000125" + "val" : "FMA:85521" }, { - "val" : "FMA:69071" + "val" : "GAID:1311" }, { - "val" : "GAID:1305" + "val" : "MAT:0000281" }, { - "val" : "MAT:0000175" + "val" : "MESH:D009672" }, { - "val" : "MESH:D004707" + "val" : "NCIT:C12463" }, { - "val" : "MIAA:0000175" + "val" : "SCTID:308820002" }, { - "val" : "NCIT:C12706" + "val" : "TAO:0000135" }, { - "val" : "SCTID:362855003" + "val" : "UMLS:C0028439" }, { - "val" : "TAO:0000017" + "val" : "VHOG:0000199" }, { - "val" : "UMLS:C0014144" + "val" : "VSAO:0000032" }, { - "val" : "VHOG:0000154" + "val" : "Wikipedia:Notochord" }, { - "val" : "Wikipedia:Endoderm" + "val" : "XAO:0000055" }, { - "val" : "XAO:0000090" + "val" : "ZFA:0000135" }, { - "val" : "ZFA:0000017" + "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "lbl" : "mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002329", + "lbl" : "somite", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The middle germ layer of the embryo, between the endoderm and ectoderm.", - "xrefs" : [ "Wikipedia:Mesoderm" ] + "val" : "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.", + "xrefs" : [ "DOI:10.1111/j.1439-0426.2012.01987.x", "Wikipedia:Somite" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "embryonic mesoderm", - "xrefs" : [ "VHOG:0000152" ] + "pred" : "hasBroadSynonym", + "val" : "mesodermal cluster", + "xrefs" : [ "GO:0001756" ] }, { "pred" : "hasRelatedSynonym", - "val" : "entire mesoderm", - "xrefs" : [ "SCTID:362854004", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "epimere", + "xrefs" : [ "ISBN:0073040584" ] }, { "pred" : "hasRelatedSynonym", - "val" : "mesodermal mantle" - } ], - "xrefs" : [ { - "val" : "AAO:0000304" - }, { - "val" : "BILA:0000037" - }, { - "val" : "BTO:0000839" + "val" : "epimere mesoderm" }, { - "val" : "CALOHA:TS-0623" + "pred" : "hasRelatedSynonym", + "val" : "epithelial somite", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] }, { - "val" : "EFO:0001981" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "somites" }, { - "val" : "EHDAA2:0001128" + "pred" : "hasRelatedSynonym", + "val" : "somitic mesoderm" }, { - "val" : "EHDAA:124" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "somitus", + "xrefs" : [ "Wikipedia:Somite" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010569" }, { - "val" : "EHDAA:160" + "val" : "AEO:0001015" }, { - "val" : "EHDAA:183" + "val" : "BTO:0001558" }, { - "val" : "EMAPA:16083" + "val" : "EHDAA2:0003436" }, { - "val" : "EV:0100006" + "val" : "EHDAA:366" }, { - "val" : "FBbt:00000126" + "val" : "EHDAA:699" }, { - "val" : "FMA:69072" + "val" : "EMAPA:31169" }, { - "val" : "GAID:522" + "val" : "FMA:85522" }, { - "val" : "MAT:0000174" + "val" : "GAID:1306" }, { - "val" : "MESH:D008648" + "val" : "MAT:0000068" }, { - "val" : "MIAA:0000174" + "val" : "MESH:D019170" }, { - "val" : "NCIT:C12750" + "val" : "MIAA:0000068" }, { - "val" : "SCTID:362854004" + "val" : "NCIT:C34302" }, { - "val" : "TAO:0000041" + "val" : "TAO:0000155" }, { - "val" : "UMLS:C0025485" + "val" : "UMLS:C0376449" }, { - "val" : "VHOG:0000152" + "val" : "VHOG:0000191" }, { - "val" : "Wikipedia:Mesoderm" + "val" : "Wikipedia:Somite" }, { - "val" : "XAO:0000050" + "val" : "XAO:0000058" }, { - "val" : "ZFA:0000041" + "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "lbl" : "stomodeum", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "lbl" : "neural crest", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anterior part of the embryonic digestive tract that develops into a mouth. 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In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasExactSynonym", + "val" : "muscular tissue" }, { - "val" : "GAID:174" + "pred" : "hasExactSynonym", + "val" : "portion of muscle tissue", + "xrefs" : [ "FMA:9641" ] }, { - "val" : "MA:0000072" + "pred" : "hasExactSynonym", + "val" : "textus muscularis" + } ], + "xrefs" : [ { + "val" : "AAO:0000306" }, { - "val" : "MAT:0000036" + "val" : "AEO:0000122" }, { - "val" : "MESH:D006321" + "val" : "CALOHA:TS-0642" }, { - "val" : "MIAA:0000036" + "val" : "EHDAA2:0003122" }, { - "val" : "NCIT:C12727" + "val" : "EMAPA:32715" }, { - "val" : "SCTID:302509004" + "val" : "FMA:9641" }, { - "val" : "TAO:0000114" + "val" : "MA:0002437" }, { - "val" : "UMLS:C0018787" + "val" : "MESH:D009132" }, { - "val" : "VHOG:0000276" + "val" : "NCIT:C12435" }, { - "val" : "Wikipedia:Heart" + "val" : "SCTID:91727004" }, { - "val" : "XAO:0000064" + "val" : "UMLS:C2328219" }, { - "val" : "ZFA:0000114" + "val" : "Wikipedia:Muscle_tissue" }, { - "val" : "galen:Heart" + "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6239" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000955", - "lbl" : "brain", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", + "lbl" : "hematopoietic system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. 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"val" : "SCTID:258335003" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002506", + "lbl" : "iris epithelium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelium that is part of a iris [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "epithelial tissue of iris", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "TAO:0000008" + "pred" : "hasExactSynonym", + "val" : "epithelium of iris", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "UMLS:C0006104" + "pred" : "hasExactSynonym", + "val" : "epithelium pigmentosum (iris)", + "xrefs" : [ "FMA:58517" ] }, { - "val" : "UMLS:C1269537" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "epithelium pigmentosum iridis", + "xrefs" : [ "FMA:58517", "FMA:TA" ] }, { - 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}, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000957", - "lbl" : "lamina", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", + "lbl" : "epiblast (generic)", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any thin layer or plate.", - "xrefs" : [ "Wikipedia:Lamina_of_the_vertebral_arch" ] + "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", + "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "laminar tissue" + "val" : "epiblast", + "xrefs" : [ "VHOG:0000243" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastocyst" + }, { + "pred" : "hasRelatedSynonym", + "val" : "ectoblast", + "xrefs" : [ "MP:0003886" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "epiblastus", + "xrefs" : [ "Wikipedia:Epiblast" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "primitive ectoderm", + "xrefs" : [ "VHOG:0000243" ] } ], "xrefs" : [ { - "val" : "Wikipedia:Lamina_of_the_vertebral_arch" + "val" : "BTO:0004593" + }, { + "val" : "FMA:296704" + }, { + "val" : "MAT:0000067" + }, { + "val" : "MIAA:0000067" + }, { + "val" : "VHOG:0000243" + }, { + "val" : "Wikipedia:Epiblast" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - merge with cell layer?" + "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. 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With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.", + "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK53175/", "https://github.com/obophenotype/uberon/issues/135", "https://github.com/seger/aao/issues/4", "https://orcid.org/0000-0002-6601-2165", "https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "chiasma opticum", - "xrefs" : [ "Wikipedia:Optic_chiasm" ] + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "pred" : "hasBroadSynonym", + "val" : "ectodermal placode", + "xrefs" : [ "FMA:293966", "PMID:22512454" ] }, { - "pred" : "hasExactSynonym", - "val" : "decussation of optic nerve fibers", - "xrefs" : [ "FMA:62045" ] + "pred" : "hasBroadSynonym", + "val" : "placode", + "xrefs" : [ "Wikipedia:Placode" ] }, { "pred" : "hasExactSynonym", - "val" : "optic chiasm", - "xrefs" : [ "Wikipedia:Optic_chiasm" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "chiasma", - "xrefs" : [ "NeuroNames:459" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "chiasma nervorum opticorum", - "xrefs" : [ "NeuroNames:459" ] + "val" : "ectodermal cranial placode", + "xrefs" : [ "UBERON:cjm" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "optic chiasm (Rufus of Ephesus)", - "xrefs" : [ "NeuroNames:459" ] + "val" : "cranial placodes", + "xrefs" : [ "XAO:0000305" ] } ], "xrefs" : [ { - "val" : "AAO:0010622" - }, { - "val" : "BAMS:DC" - }, { - "val" : "BAMS:OC" - }, { - "val" : "BAMS:och" - }, { - "val" : "BAMS:ox" - }, { - "val" : "BIRNLEX:1416" + "val" : "AAO:0010466" }, { - "val" : "BM:Tel-OCX" + "val" : "EFO:0001650" }, { - "val" : "DHBA:10644" + "val" : "MAT:0000369" }, { - "val" : "DMBA:17783" + "val" : "MIAA:0000369" }, { - "val" : "EHDAA2:0001302" + "val" : "XAO:0000305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not merge with neurogenic placode" }, { - "val" : "EHDAA:10227" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", + "lbl" : "anatomical cavity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", + "xrefs" : [ "FMA:67552" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cavity" + } ], + "xrefs" : [ { + "val" : "BIRNLEX:1011" }, { - "val" : "EMAPA:17603" + "val" : "EMAPA:37442" }, { - "val" : "FMA:62045" + "val" : "FMA:67552" }, { - "val" : "GAID:832" + "val" : "MA:0002447" }, { - "val" : "HBA:9310" + "val" : "NCIT:C34007" }, { - "val" : "MA:0001098" + "val" : "galen:Cavity" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002616", + "lbl" : "regional part of brain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. 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Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", + "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] }, - "comments" : [ "Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. 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Contrast with parenchyma.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "facia/facies", - "xrefs" : [ "Wikipedia:Face" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "visage", - "xrefs" : [ "BTO:0003369" ] + "val" : "stromal connective tissue" } ], "xrefs" : [ { - "val" : "BTO:0003369" - }, { - "val" : "CALOHA:TS-2216" - }, { - "val" : "EMAPA:32763" - }, { - "val" : "FMA:24728" - }, { - "val" : "GAID:64" - }, { - "val" : "HAO:0000316" - }, { - "val" : "MA:0002473" - }, { - "val" : "MESH:D005145" - }, { - "val" : "NCIT:C13071" - }, { - "val" : "SCTID:302549007" - }, { - "val" : "UMLS:C0015450" + "val" : "FMA:81494" }, { - "val" : "Wikipedia:Face" + "val" : "NCIT:C67387" }, { - "val" : "galen:Face" + "val" : "UMLS:C0927195" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "lbl" : "digestive tract", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003902", + "lbl" : "retinal neural layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A tube extending from the mouth to the anus.", - "xrefs" : [ "Wikipedia:Talk:Human_gastrointestinal_tract", "https://github.com/geneontology/go-ontology/issues/7549" ] + "val" : "The part of the retina that contains neurons and photoreceptor cells[GO].", + "xrefs" : [ "GO:0003407" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "gut" - }, { "pred" : "hasExactSynonym", - "val" : "digestive tube" + "val" : "neural layer of retina", + "xrefs" : [ "FMA:58628" ] }, { "pred" : "hasExactSynonym", - "val" : "enteric tract", - "xrefs" : [ "ZFA:0000112" ] + "val" : "neural retina", + "xrefs" : [ "XAO:0003216", "ZFA:0000046" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary canal" + "pred" : "hasExactSynonym", + "val" : "neuroretina", + "xrefs" : [ "ZFA:0000046" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary tract" + "pred" : "hasExactSynonym", + "val" : "stratum nervosum (retina)", + "xrefs" : [ "FMA:58628" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "digestive canal", - "xrefs" : [ "BTO:0000058" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "stratum nervosum retinae", + "xrefs" : [ "FMA:58628", "FMA:TA" ] }, { "pred" : "hasRelatedSynonym", - "val" : "gut tube" + "val" : "neural retinal epithelium", + "xrefs" : [ "MA:000027" ] } ], "xrefs" : [ { - "val" : "AAO:0010023" - }, { - "val" : "BILA:0000083" - }, { - "val" : "BTO:0000511" - }, { - "val" : "BTO:0000545" + "val" : "AAO:0011095" }, { - "val" : "EHDAA2:0000726" + "val" : "BTO:0000929" }, { - "val" : "EHDAA:518" + "val" : "CALOHA:TS-0685" }, { - "val" : "EMAPA:16247" + "val" : "EHDAA2:0001253" }, { - "val" : "FBbt:00003125" + "val" : "EHDAA:4763" }, { - "val" : "FMA:45615" + "val" : "EMAPA:17171" }, { - "val" : "MA:0000917" + "val" : "EMAPA:18590" }, { - "val" : "NCIT:C34082" + "val" : "FMA:58628" }, { - "val" : "TAO:0000112" + "val" : "MA:0000277" }, { - "val" : "TGMA:0001819" + "val" : "NCIT:C33166" }, { - "val" : "UMLS:C0017189" + "val" : "TAO:0000046" }, { - "val" : "VHOG:0000309" + "val" : "UMLS:C1518263" }, { - "val" : "WBbt:0005743" + "val" : "VHOG:0000535" }, { - "val" : "ZFA:0000112" + "val" : "XAO:0003216" }, { - "val" : "galen:AlimentaryTract" + "val" : "ZFA:0000046" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_41324" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -21394,98 +24561,97 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001605", - "lbl" : "ciliary muscle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", + "lbl" : "epithelial tube", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].", - "xrefs" : [ "Wikipedia:Ciliary_muscle" ] + "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", + "xrefs" : [ "GO:0060562", "PMID:12526790" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "musculus ciliarus", - "xrefs" : [ "BTO:0000654" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bowman`s muscles", - "xrefs" : [ "BTO:0000654" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ciliaris", - "xrefs" : [ "Wikipedia:Ciliary_muscle" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "musculus ciliaris", - "xrefs" : [ "Wikipedia:Ciliary_muscle" ] + "val" : "epithelial or endothelial tube" } ], "xrefs" : [ { - "val" : "BTO:0000654" - }, { - "val" : "EMAPA:35240" - }, { - "val" : "FMA:49151" - }, { - "val" : "MA:0001269" - }, { - "val" : "NCIT:C32315" - }, { - "val" : "SCTID:280862009" + "val" : "AEO:0000114" }, { - "val" : "UMLS:C0559230" + "val" : "EHDAA2:0003114" }, { - "val" : "Wikipedia:Ciliary_muscle" + "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001630", - "lbl" : "muscle organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003931", + "lbl" : "diencephalic white matter", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].", - "xrefs" : [ "GO:0007517" ] + "val" : "White matter that is part of a diencephalon [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "muscle", - "xrefs" : [ "ZFA:0005145" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37474" - }, { - "val" : "EV:0100146" + "pred" : "hasExactSynonym", + "val" : "diencephalic tract/commissure", + "xrefs" : [ "ZFA:0000338" ] }, { - "val" : "FMA:5022" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "diencephalic tracts and commissures", + "xrefs" : [ "TAO:0000338" ] }, { - "val" : "GAID:131" + "pred" : "hasExactSynonym", + "val" : "predominantly white regional part of diencephalon", + "xrefs" : [ "BIRNLEX:1678" ] }, { - "val" : "MA:0000015" + "pred" : "hasExactSynonym", + "val" : "white matter of diencephalon", + "xrefs" : [ "FMA:83931" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:1678" }, { - "val" : "SCTID:71616004" + "val" : "FMA:83931" }, { - "val" : "TAO:0005145" + "val" : "TAO:0000338" }, { - "val" : "VHOG:0001245" + "val" : "ZFA:0000338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0023148" }, { - "val" : "XAO:0000172" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004022", + "lbl" : "germinal neuroepithelium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.", + "xrefs" : [ "MP:0004261", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "germinal neuroepithelial layer", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "ZFA:0005145" + "pred" : "hasExactSynonym", + "val" : "germinal neuroepithelium", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { - "val" : "galen:Muscle" + "pred" : "hasExactSynonym", + "val" : "original neural tube", + "xrefs" : [ "NCBIBook:NBK10047" ] } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -21493,874 +24659,834 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001711", - "lbl" : "eyelid", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004060", + "lbl" : "neural tube ventricular layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.", + "xrefs" : [ "MP:0009689", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blepharon" + "pred" : "hasBroadSynonym", + "val" : "ependymal layer", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { "pred" : "hasExactSynonym", - "val" : "eye lid" + "val" : "neural tube ependymal layer", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { "pred" : "hasExactSynonym", - "val" : "palpebra" + "val" : "neural tube ventricular germinal zone", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "blephara" + "pred" : "hasExactSynonym", + "val" : "neural tube ventricular zone", + "xrefs" : [ "MP:0009689" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "palpebrae" + "pred" : "hasNarrowSynonym", + "val" : "neural tube ependymal zone", + "xrefs" : [ "MP:0009689" ] } ], "xrefs" : [ { - "val" : "BTO:0002241" - }, { - "val" : "EHDAA2:0000487" - }, { - "val" : "EHDAA:9037" - }, { - "val" : "EMAPA:17829" - }, { - "val" : "EV:0100338" - }, { - "val" : "FMA:54437" - }, { - "val" : "GAID:72" - }, { - "val" : "MA:0000268" - }, { - "val" : "MESH:D005143" - }, { - "val" : "NCIT:C12713" - }, { - "val" : "SCTID:265782007" + "val" : "EMAPA:17152" }, { - "val" : "UMLS:C0015426" + "val" : "EMAPA:35362" }, { - "val" : "VHOG:0000016" + "val" : "EMAPA_RETIRED:16783" }, { - "val" : "Wikipedia:Eyelid" + "val" : "MA:0003193" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001766", - "lbl" : "anterior chamber of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004061", + "lbl" : "neural tube mantle layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.", - "xrefs" : [ "MESH:A09.371.060.067", "MP:0005205" ] + "val" : "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.", + "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "anterior chamber", - "xrefs" : [ "HP:0000593", "MP:0010709" ] + "val" : "neural tube intermediate zone", + "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] }, { - "pred" : "hasExactSynonym", - "val" : "anterior chamber of eye" + "pred" : "hasRelatedSynonym", + "val" : "future brain marginal layer", + "xrefs" : [ "EMAPA:35360" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:17148" }, { - "pred" : "hasExactSynonym", - "val" : "camera anterior" + "val" : "EMAPA:35360" }, { + "val" : "neuronames:1367" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004062", + "lbl" : "neural tube marginal layer", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.", + "xrefs" : [ "MP:0009691", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "eye anterior chamber" - }, { - "pred" : "hasRelatedSynonym", - "val" : "camera anterior bulbi", - "xrefs" : [ "BTO:0002084" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "camera anterior bulbi oculi", - "xrefs" : [ "Wikipedia:Anterior_chamber_of_eyeball" ] + "val" : "neural tube marginal zone", + "xrefs" : [ "MP:0009691" ] }, { "pred" : "hasRelatedSynonym", - "val" : "camera oculi anterior", - "xrefs" : [ "BTO:0002084" ] + "val" : "brain marginal zone" } ], "xrefs" : [ { - "val" : "BTO:0002084" - }, { - "val" : "EHDAA2:0000129" - }, { - "val" : "EHDAA:9033" - }, { - "val" : "EMAPA:18231" - }, { - "val" : "FMA:58078" - }, { - "val" : "GAID:889" - }, { - "val" : "MA:0000262" - }, { - "val" : "MESH:D000867" - }, { - "val" : "NCIT:C12667" - }, { - "val" : "SCTID:181160009" - }, { - "val" : "UMLS:C0003151" - }, { - "val" : "VHOG:0001431" + "val" : "EMAPA:17151" }, { - "val" : "Wikipedia:Anterior_chamber_of_eyeball" + "val" : "neuronames:1368" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - 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"val" : "tunica vasculosa of eyeball", - "xrefs" : [ "FMA:58103" ] + "val" : "content of orbital part of eye", + "xrefs" : [ "FMA:260119" ] }, { "pred" : "hasExactSynonym", - "val" : "uvea", - "xrefs" : [ "FMA:58103" ] + "val" : "eye region", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "uveal tract", - "xrefs" : [ "FMA:58103" ] + "val" : "orbital part of face", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "pars iridica retinae", - "xrefs" : [ "Wikipedia:Uvea" ] + "val" : "ocular and peri-ocular region" }, { "pred" : "hasRelatedSynonym", - "val" : "tunica vasculatis oculi", - "xrefs" : [ "Wikipedia:Uvea" ] + "val" : "ocular region" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "tunica vasculosa bulbi", - "xrefs" : [ "Wikipedia:Uvea" ] + "val" : "orbital content", + "xrefs" : [ "FMA:260119" ] }, { "pred" : "hasRelatedSynonym", - 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Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].", + "xrefs" : [ "GO:0003404", "Wikipedia:Optic_vesicles" ] + }, + "comments" : [ "Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 \"Developmental Biology\"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "endothelium anterius corneae", - "xrefs" : [ "BTO:0000287" ] + "val" : "evagination" }, { "pred" : "hasRelatedSynonym", - "val" : "endothelium camerae anterioris bulbi", - "xrefs" : [ "BTO:0000287" ] + "val" : "eye vesicle", + "xrefs" : [ "XAO:0000228" ] }, { "pred" : "hasRelatedSynonym", - "val" : "endothelium corneale", - "xrefs" : [ "BTO:0000287" ] + "val" : "ocular vesicle", + "xrefs" : [ "VHOG:0000165" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "epithelium posterius corneae", - "xrefs" : [ "BTO:0000287" ] + "val" : "optic vesicles", + "xrefs" : [ "ZFA:0000050" ] } ], "xrefs" : [ { - "val" : "BTO:0000287" - }, { - "val" : "CALOHA:TS-0173" - }, { - "val" : "EFO:0001917" - }, { - "val" : "EHDAA2:0000319" + "val" : "AAO:0011039" }, { - "val" : "EMAPA:17162" + "val" : "EHDAA2:0001320" }, { - "val" : "FMA:58263" + "val" : "EMAPA:16540" }, { - "val" : "GAID:895" + "val" : "FMA:293357" }, { - "val" : "MA:0001243" + "val" : "NCIT:C34236" }, { - "val" : "MESH:D019573" + "val" : "SCTID:362864008" }, { - "val" : "NCIT:C12928" + "val" : "TAO:0000050" }, { - "val" : "SCTID:368825001" + "val" : "UMLS:C0231106" }, { - "val" : "TAO:0002187" + "val" : "VHOG:0000165" }, { - "val" : "UMLS:C0459875" + "val" : "Wikipedia:Optic_vesicles" }, { - "val" : "Wikipedia:Corneal_epithelium" + "val" : "XAO:0000228" }, { - "val" : "ZFA:0001683" + "val" : "ZFA:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001773", - "lbl" : "sclera", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", + "lbl" : "cardiogenic plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].", - "xrefs" : [ "Wikipedia:Sclera", "ZFIN:ZDB-PUB-050701-15" ] + "val" : "The first recognizable structure derived from the heart field.", + "xrefs" : [ "GO:0003142" ] }, - "comments" : [ "Disease notes: implicated in rheumatoid arthritis." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "scleral capsule" - } ], - "xrefs" : [ { - "val" : "AAO:0010354" - }, { - "val" : "BTO:0001606" - }, { - "val" : "EMAPA:19027" - }, { - "val" : "EV:0100342" - }, { - "val" : "FMA:58269" - }, { - "val" : "GAID:911" - }, { - "val" : "MA:0000280" - }, { - "val" : "MESH:D012590" - }, { - "val" : "NCIT:C12784" - }, { - "val" : "SCTID:181163006" + "pred" : "hasExactSynonym", + "val" : "myocardial plate", + "xrefs" : [ "EHDAA2:0000215" ] }, { - "val" : "UMLS:C0036410" + "pred" : "hasRelatedSynonym", + "val" : "cardiac crescent", + "xrefs" : [ "EMAPA:16106" ] }, { - "val" : "VHOG:0001274" + "pred" : "hasRelatedSynonym", + "val" : "cardiogenic crescent", + "xrefs" : [ "GO:0003142" ] }, { - "val" : "Wikipedia:Sclera" + "pred" : "hasRelatedSynonym", + "val" : "heart rudiment" + } ], + "xrefs" : [ { + "val" : "EHDAA2:0000215" }, { - "val" : "XAO:0000183" + "val" : "EMAPA:16106" }, { - "val" : "ZFA:0005563" + "val" : "VHOG:0000975" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. 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Along with the ciliary body and iris, the choroid forms the uveal tract[WP].", - "xrefs" : [ "Wikipedia:Choroid" ] + "val" : "An epithelial tube that will give rise to the mature heart.", + "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "choroid", - "xrefs" : [ "MA:0000263" ] - }, { - "pred" : "hasExactSynonym", - "val" : "choroid coat", - "xrefs" : [ "Wikipedia:Choroid" ] - }, { - "pred" : "hasExactSynonym", - "val" : "choroidea", - "xrefs" : [ "Wikipedia:Choroid" ] + "val" : "embryonic heart tube", + "xrefs" : [ "GO:0003143" ] }, { "pred" : "hasExactSynonym", - "val" : "eye choroid", - "xrefs" : [ "VHOG:0001568" ] + "val" : "endocardial heart tube", + "xrefs" : [ "MP:0012700" ] }, { "pred" : "hasExactSynonym", - "val" : "posterior uvea", - "xrefs" : [ "Wikipedia:Uvea#Regions" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "chorioid", - "xrefs" : [ "BTO:0001829" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "choroidea", - "xrefs" : [ "Wikipedia:Choroid" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "optic choroid", - "xrefs" : [ "ZFA:0005229" ] + "val" : "endocardial tube", + "xrefs" : [ "XAO:0000337" ] } ], "xrefs" : [ { - "val" : "BTO:0001829" - }, { - "val" : "CALOHA:TS-2054" - }, { - "val" : "EMAPA:19077" - }, { - "val" : "EV:0100347" - }, { - "val" : "FMA:58298" + "val" : "AAO:0010411" }, { - "val" : "GAID:913" + "val" : "EFO:0003526" }, { - "val" : "MA:0000263" + "val" : "EMAPA:32685" }, { - "val" : "MESH:D002829" + "val" : "NCIT:C34161" }, { - "val" : "NCIT:C12344" + "val" : "TAO:0000360" }, { - "val" : "SCTID:181172003" + "val" : "XAO:0000337" }, { - "val" : "TAO:0005229" + "val" : "ZFA:0000360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "lbl" : "cardiac chamber", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", + "xrefs" : [ "GO:0003205" ] + }, + "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "chamber of heart" }, { - "val" : "UMLS:C0008520" + "pred" : "hasExactSynonym", + "val" : "heart chamber" + } ], + "xrefs" : [ { + "val" : "FMA:7095" }, { - "val" : "VHOG:0001568" + "val" : "SCTID:276456008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004277", + "lbl" : "eye muscle", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A muscle that is part of the eye region.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "AAO:0000156" }, { - "val" : "Wikipedia:Choroid" + "val" : "EMAPA:35335" }, { - "val" : "ZFA:0005229" + "val" : "MA:0000271" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. 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The heart rudiment is the first structure of the heart tube.", + "xrefs" : [ "GO:0003313" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "ciliary body epithelium", - "xrefs" : [ "FMA:58464" ] - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of ciliary body", - "xrefs" : [ "FMA:58464" ] + "val" : "heart cone", + "xrefs" : [ "GO:0003313" ] }, { "pred" : "hasExactSynonym", - "val" : "ocular ciliary epithelium" + "val" : "rudimentary heart", + "xrefs" : [ "ZFA:0000115" ] } ], "xrefs" : [ { - "val" : "BTO:0001770" - }, { - "val" : "CALOHA:TS-0695" - }, { - "val" : "EMAPA:35239" - }, { - "val" : "FMA:58464" - }, { - "val" : "MA:0001238" + "val" : "TAO:0000115" }, { - "val" : "NCIT:C32314" + "val" : "ZFA:0000115" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004348", + "lbl" : "optic eminence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The embryonic structure that gives rise to the corneal ectoderm.", + "xrefs" : [ "MP:0006305" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "EHDAA:938" }, { - "val" : "SCTID:280870004" + "val" : "EMAPA:16322" }, { - "val" : "UMLS:C0459736" + "val" : "RETIRED_EHDAA2:0001308" }, { - "val" : "Wikipedia:Ciliary_body#Ciliary_epithelium" + "val" : "VHOG:0001296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001781", - "lbl" : "layer of retina", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004367", + "lbl" : "Descemet's membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the layers that make up the retina[MP].", - "xrefs" : [ "MP:0003727" ] + "val" : "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].", + "xrefs" : [ "MP:0004285", "https://github.com/obophenotype/uberon/issues/15" ] }, + "comments" : [ "The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)" ], "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "retina layer" + "val" : "Descemet membrane" }, { "pred" : "hasExactSynonym", - "val" : "retina neuronal layer", - "xrefs" : [ "MP:0006069" ] + "val" : "Descemet's posterior elastic lamina", + "xrefs" : [ "FMA:58309" ] }, { "pred" : "hasExactSynonym", - "val" : "retinal layer" + "val" : "lamina limitans posterior", + "xrefs" : [ "FMA:58309" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "retinal neuronal layer", - "xrefs" : [ "MP:0006069" ] + "val" : "lamina limitans posterior corneae", + "xrefs" : [ "FMA:58309", "FMA:TA" ] + }, { + "pred" : "hasExactSynonym", + "val" : "posterior limiting lamina", + "xrefs" : [ "MA:0001246" ] + }, { + "pred" : "hasExactSynonym", + "val" : "posterior limiting lamina of cornea", + "xrefs" : [ "FMA:58309" ] + }, { + "pred" : "hasExactSynonym", + "val" : "posterior limiting membrane", + "xrefs" : [ "ZFA:0001686" ] } ], "xrefs" : [ { - 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Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001795", - "lbl" : "inner plexiform layer of retina", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", + "lbl" : "muscle structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia).", - "xrefs" : [ "NLX:20558" ] + "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", + "xrefs" : [ "GO:0061061" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "retina inner plexiform layer" - }, { - "pred" : "hasExactSynonym", - "val" : "retinal inner plexiform layer" - }, { - "pred" : "hasExactSynonym", - "val" : "stratum plexiforme internum", - "xrefs" : [ "FMA:58704" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasNarrowSynonym", - "val" : "IPL" - }, { - "pred" : "hasRelatedSynonym", - "val" : "inner plexiform layer", - "xrefs" : [ "BTO:0003175" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "internal plexiform layer of retina", - "xrefs" : [ "NLXANAT:1005032" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "retina, inner plexiform layer", - "xrefs" : [ "BAMS:Ripl" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "retinal internal plexiform layer", - "xrefs" : [ "NLXANAT:1005032" ] + "val" : "musculus", + "xrefs" : [ "FMA:30316" ] }, { "pred" : "hasRelatedSynonym", - "val" : "stratum plexifome internum", - "xrefs" : [ "BTO:0003175" ] + "val" : "muscle" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "stratum plexiforme internum retinae", - "xrefs" : [ "Wikipedia:Inner_plexiform_layer" ] + "val" : "muscle element" } ], "xrefs" : [ { - "val" : "BAMS:Ripl" - }, { - "val" : "BTO:0003175" - }, { - "val" : "EMAPA:35741" - }, { - "val" : "FMA:58704" - }, { - "val" : "MA:0001312" - }, { - "val" : "NCIT:C32809" - }, { - "val" : "NLX:20558" - }, { - "val" : "NLXANAT:1005032" - }, { - "val" : "SCTID:280682006" - }, { - "val" : "TAO:0001329" - }, { - "val" : "UMLS:C0229221" - }, { - "val" : "VHOG:0001168" - }, { - "val" : "Wikipedia:Inner_plexiform_layer" - }, { - "val" : "XAO:0003225" - }, { - "val" : "ZFA:0001329" + "val" : "FMA:30316" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001796", - "lbl" : "aqueous humor of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", + "lbl" : "epithelial fold", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A thick watery refractive medium that fills the space between the lens and the cornea[WP].", - "xrefs" : [ "Wikipedia:Aqueous_humor" ] + "val" : "An epithelial sheet bent on a linear axis.", + "xrefs" : [ "GO:0060571" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005162", + "lbl" : "multi cell part structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.", + "xrefs" : [ "CARO:0001000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "aqueous humor" + "val" : "multi-cell-component structure", + "xrefs" : [ "CARO:0001000" ] }, { "pred" : "hasExactSynonym", - "val" : "aqueous humour", - "xrefs" : [ "EHDAA2:0000139" ] + "val" : "multi-cell-part structure", + "xrefs" : [ "CARO:0001000" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "humor aquosus", - "xrefs" : [ "FMA:58819", "FMA:TA" ] + "pred" : "hasRelatedSynonym", + "val" : "cell part cluster", + "xrefs" : [ "FMA:83115" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0000139" - }, { - "val" : "EHDAA:10196" - }, { - "val" : "EMAPA:18232" - }, { - "val" : "ENVO:02000024" - }, { - "val" : "FMA:58819" - }, { - "val" : "GAID:890" - }, { - "val" : "MA:0001236" - }, { - "val" : "MESH:D001082" - }, { - "val" : "NCIT:C13190" - }, { - "val" : "SCTID:280587006" - }, { - "val" : "UMLS:C0003662" + "val" : "AAO:0011000" }, { - "val" : "VHOG:0000548" + "val" : "CARO:0001000" }, { - "val" : "Wikipedia:Aqueous_humor" + "val" : "FBbt:00007060" }, { - "val" : "ZFA:0005564" + "val" : "FMA:83115" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001797", - "lbl" : "vitreous humor", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005174", + "lbl" : "dorsal region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.", - "xrefs" : [ "MP:0002699" ] + "val" : "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "portion of vitreous humor", - "xrefs" : [ "FMA:67388" ] - }, { - "pred" : "hasExactSynonym", - "val" : "humor vitreous" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "humor vitreus", - "xrefs" : [ "FMA:58822", "FMA:TA" ] - }, { "pred" : "hasExactSynonym", - "val" : "vitreous", - "xrefs" : [ "ZFA:0005561" ] + "val" : "back organ", + "xrefs" : [ "MA:0001901" ] }, { "pred" : "hasExactSynonym", - "val" : "whole portion of vitreous humor", - "xrefs" : [ "FMA:58822" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "humoral fluid", - "xrefs" : [ "BTO:0001451" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular fluid", - "xrefs" : [ "BTO:0001451" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "vitreous fluid", - "xrefs" : [ "BTO:0001451" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "vitreous humour" + "val" : "dorsal region organ" } ], "xrefs" : [ { - "val" : "BTO:0001451" - }, { - "val" : "CALOHA:TS-0308" - }, { - "val" : "EMAPA:17837" - }, { - "val" : "ENVO:02000032" - }, { - "val" : "EV:0100344" - }, { - "val" : "FMA:58822" - }, { - "val" : "MA:0001286" - }, { - "val" : "NCIT:C13323" - }, { - "val" : "UMLS:C0229096" - }, { - "val" : "VHOG:0000795" - }, { - "val" : "Wikipedia:Vitreous_humour" + "val" : "EMAPA:37274" }, { - "val" : "ZFA:0005561" + "val" : "MA:0001901" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001798", - "lbl" : "vitreous body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", + "lbl" : "trunk region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified].", - "xrefs" : [ "MP:0002699" ] + "val" : "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "trunk organ", + "xrefs" : [ "MA:0000516" ] + } ], "xrefs" : [ { - "val" : "CALOHA:TS-0308" - }, { - "val" : "FMA:58827" - }, { - "val" : "GAID:919" - }, { - "val" : "MA:0002462" - }, { - "val" : "MESH:D014822" - }, { - "val" : "NCIT:C33884" - }, { - "val" : "SCTID:181170006" + "val" : "EMAPA:37270" }, { - "val" : "UMLS:C0042905" + "val" : "MA:0000516" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001799", - "lbl" : "vitreous chamber of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005178", + "lbl" : "thoracic cavity element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified].", - "xrefs" : [ "BTO:0002087" ] + "val" : "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "camera postrema", - "xrefs" : [ "FMA:58848" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "camera postrema bulbi oculi", - "xrefs" : [ "FMA:58848", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "camera vitrea", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "camera vitrea bulbi", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "postremal chamber", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "postremal chamber of eyeball", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "vitreous chamber", - "xrefs" : [ "FMA:58848" ] + "val" : "thoracic cavity organ", + "xrefs" : [ "MA:0000557" ] } ], "xrefs" : [ { - "val" : "BTO:0002087" - }, { - "val" : "EMAPA:37805" - }, { - "val" : "FMA:58848" - }, { - "val" : "MA:0002461" - }, { - "val" : "NCIT:C33885" - }, { - "val" : "UMLS:C0229095" + "val" : "EMAPA:37273" }, { - "val" : "Wikipedia:Vitreous_chamber" + "val" : "MA:0000557" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -23352,273 +26308,152 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "lbl" : "anterior segment of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", + "lbl" : "thoracic segment organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).", - "xrefs" : [ "ISBN:0-683-40008-8", "MESH:A09.371.060", "MP:0005193" ] + "val" : "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "anterior eye segment" - }, { - "pred" : "hasExactSynonym", - "val" : "anterior segment eye", - "xrefs" : [ "ZFA:0005566" ] - }, { - "pred" : "hasExactSynonym", - "val" : "anterior segment of eye" - }, { - "pred" : "hasExactSynonym", - "val" : "anterior segment of the eye" - }, { - "pred" : "hasExactSynonym", - "val" : "eye anterior segment" - }, { - "pred" : "hasExactSynonym", - "val" : "segmentum anterius (bulbus oculi)" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "segmentum anterius bulbi oculi", - "xrefs" : [ "Wikipedia:Anterior_segment_of_eyeball" ] + "val" : "upper body organ", + "xrefs" : [ "MA:0000563" ] } ], - "xrefs" : [ { - "val" : "EMAPA:36594" - }, { - "val" : "FMA:58865" - }, { - "val" : "MA:0002484" - }, { - "val" : "MESH:D000869" - }, { - "val" : "NCIT:C12668" - }, { - "val" : "SCTID:280658001" - }, { - "val" : "UMLS:C0003153" - }, { - "val" : "Wikipedia:Anterior_segment_of_eyeball" + "xrefs" : [ { + "val" : "EMAPA:37271" }, { - "val" : "ZFA:0005566" + "val" : "MA:0000563" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001802", - "lbl" : "posterior segment of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005253", + "lbl" : "head mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive).", - "xrefs" : [ "ISBN:0-683-40008-8", "MP:0005195" ] + "val" : "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.", + "xrefs" : [ "ISBN:0683400088", "MP:0011260" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "eye posterior segment" - }, { - "pred" : "hasExactSynonym", - "val" : "posterior eye segment" - }, { - "pred" : "hasExactSynonym", - "val" : "posterior segment eye", - "xrefs" : [ "ZFA:0005567" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior segment of eye" - }, { - "pred" : "hasExactSynonym", - "val" : "posterior segment of the eye" + "val" : "cephalic mesenchyme", + "xrefs" : [ "MP:0011260" ] }, { - "pred" : "hasExactSynonym", - "val" : "segmentum posterius (bulbus oculi)" + "pred" : "hasRelatedSynonym", + "val" : "cranial mesenchyme", + "xrefs" : [ "MGI:anna" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "pred" : "hasRelatedSynonym", - 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Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA].", + "xrefs" : [ "FMA:9689", "https://github.com/obophenotype/uberon/issues/86" ] + }, + "comments" : [ "See notes for serous membrane" ], + "xrefs" : [ { + "val" : "FMA:9689" }, { - "val" : "MESH:D008526" + "val" : "SCTID:362890006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005908", + "lbl" : "conjunctival sac", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A serous sac which is the aggregate of the conjunctiva plus the conjunctival space.", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/Serous-Membranes-Design-Pattern" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "conjunctiva serous sac" }, { - "val" : "MIAA:0000111" + "pred" : "hasNarrowSynonym", + "val" : "subbrillar sac", + "xrefs" : [ "NCBITaxon:8570" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:18233" }, { - "val" : "NCIT:C12442" + "val" : "FMA:20291" }, { - "val" : "SCTID:279104005" + "val" : "SCTID:362531001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005944", + "lbl" : "axial skeleton plus cranial skeleton", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].", + "xrefs" : [ "FMA:71221", "VSAO:0000056", "Wikipedia:Axial_skeleton", "https://github.com/obophenotype/uberon/issues/44", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "skeleton axiale", + "xrefs" : [ "Wikipedia:Axial_skeleton" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000963" }, { - "val" : "TAO:0000545" + "val" : "EMAPA:17214" }, { - "val" : "UMLS:C0025148" + "val" : "MA:0000308" }, { - "val" : "UMLS:C1269575" + "val" : "NCIT:C32172" }, { - "val" : "VHOG:0000181" + "val" : "SCTID:361725000" }, { - "val" : "Wikipedia:Bone_marrow_of_ovary_oblongata" + "val" : "UMLS:C0222645" }, { - "val" : "XAO:0003100" + "val" : "VSAO:0000056" }, { - "val" : "ZFA:0000545" + "val" : "Wikipedia:Axial_skeleton" }, { - "val" : "neuronames:698" + "val" : "XAO:0004011" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -23946,712 +27020,640 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001908", - "lbl" : "optic tract", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006134", + "lbl" : "nerve fiber", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. 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A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system.", + "xrefs" : [ "Wikipedia:Nervous_system_fiber" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "optic lemniscus" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "optic tracts", - "xrefs" : [ "ZFA:0000252" ] + "val" : "nerve fibre", + "xrefs" : [ "FMA:5914" ] }, { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tractus optici", - "xrefs" : [ "NeuroNames:460" ] + "pred" : "hasExactSynonym", + "val" : "neurofibra", + "xrefs" : [ "FMA:5914", "FMA:TA" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "neurofibrum", + "xrefs" : [ "FMA:5914" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "tractus opticus", - "xrefs" : [ "Wikipedia:Optic_tract" ] + "val" : "nerve fibers", + "xrefs" : [ "BAMS:nfi" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "visual pathway", - "xrefs" : [ "GAID:735" ] + "val" : "neurofibra", + "xrefs" : [ "Wikipedia:Nerve_fiber" ] } ], "xrefs" : [ { - "val" : "BAMS:opt" + "val" : "BAMS:nfi" }, { - "val" : "BIRNLEX:1684" + "val" : "FMA:5914" }, { - "val" : "BM:Tel-OT" + "val" : "MESH:D009412" }, { - "val" : "DHBA:10589" + "val" : "SCTID:88545005" }, { - "val" : "DMBA:17785" + "val" : "Wikipedia:Nervous_system_fiber" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "EMAPA:35617" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006135", + "lbl" : "myelinated nerve fiber", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH).", + "xrefs" : [ "ncithesaurus:Myelinated_Nerve_Fiber" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "FMA:5915" }, { - "val" : "FMA:62046" + "val" : "GAID:745" }, { - "val" : "GAID:735" + "val" : "MESH:D009413" }, { - "val" : "HBA:9309" + "val" : "NCIT:C12627" }, { - "val" : "MA:0001099" + "val" : "SCTID:362296008" }, { - "val" : "MBA:125" + "val" : "UMLS:C0027750" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adding link to UBERON:0002316 ! white matter of neuraxis" }, { - "val" : "MESH:D014795" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117569" }, { - "val" : "NCIT:C33218" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" }, { - "val" : "SCTID:280952003" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" }, { - "val" : "TAO:0000252" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006222", + "lbl" : "future diencephalon", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The foremost region of the future forebrain that develops into the diencephalon.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Diencephalon" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "presumptive diencephalon", + "xrefs" : [ "TAO:0000574" ] + } ], + "xrefs" : [ { + "val" : "EFO:0003442" }, { - "val" : "UMLS:C0152405" + "val" : "EHDAA2:0000600" }, { - "val" : "VHOG:0001164" + "val" : "EHDAA:844" }, { - "val" : "Wikipedia:Optic_tract" + "val" : "EMAPA:16514" }, { - "val" : "XAO:0004101" + "val" : "RETIRED_EHDAA2:0000386" }, { - "val" : "ZFA:0000252" + "val" : "TAO:0000574" }, { - "val" : "neuronames:460" + "val" : "ZFA:0000574" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001943", - "lbl" : "midbrain tegmentum", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006238", + "lbl" : "future brain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].", - "xrefs" : [ "FMA:FMA", "ISBN:0471888893", "Wikipedia:Midbrain_tegmentum" ] + "val" : "The embryonic precursor of the brain.", + "xrefs" : [ "NLX:94995" ] }, - "comments" : [ "'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasBroadSynonym", - "val" : "MTg", - "xrefs" : [ "BIRNLEX:1200", "NIFSTD:NeuroNames_abbrevSource" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "tegmentum", - "xrefs" : [ "ISBN:0471888893" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "tegmentum mesencephali", - "xrefs" : [ "Wikipedia:Midbrain_tegmentum" ] + "val" : "brain rudiment", + "xrefs" : [ "TAO:0000146" ] }, { "pred" : "hasExactSynonym", - "val" : "tegmentum of midbrain" + "val" : "presumptive brain", + "xrefs" : [ "ZFA:0000146" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "mesencephalic tegmentum", - "xrefs" : [ "VHOG:0001367" ] + "pred" : "hasNarrowSynonym", + "val" : "encephalon", + "xrefs" : [ "NLX:94995" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "tegmentum mesencephalicum", - "xrefs" : [ "NeuroNames:491" ] + "val" : "embryonic brain", + "xrefs" : [ "BTO:0004726" ] } ], "xrefs" : [ { - "val" : "BAMS:MTg" - }, { - "val" : "BIRNLEX:1200" - }, { - "val" : "BTO:0003388" - }, { - "val" : "DHBA:12195" - }, { - "val" : "EFO:0000921" - }, { - "val" : "EHDAA2:0004475" - }, { - "val" : "EMAPA:18215" - }, { - "val" : "FMA:62393" - }, { - "val" : "HBA:9002" - }, { - "val" : "MA:0000212" + "val" : "BAMS:Enc" }, { - "val" : "MAT:0000452" + "val" : "BTO:0004726" }, { - "val" : "SCTID:362392007" + "val" : "EFO:0003431" }, { - "val" : "TAO:0000160" + "val" : "EHDAA:300" }, { - "val" : "UMLS:C0039441" + "val" : "EHDAA:830" }, { - "val" : "VHOG:0001367" + "val" : "EMAPA:16089" }, { - "val" : "Wikipedia:Midbrain_tegmentum" + "val" : "FMA:312967" }, { - "val" : "XAO:0004271" + "val" : "RETIRED_EHDAA2:0000591" }, { - "val" : "ZFA:0000160" + "val" : "TAO:0000146" }, { - "val" : "neuronames:491" + "val" : "ZFA:0000146" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "lbl" : "blood plasma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006240", + "lbl" : "future forebrain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The liquid component of blood, in which erythrocytes are suspended.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A presumptive structure that has the potential to develop into a forebrain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "plasma", - "xrefs" : [ "MA:0002501" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "portion of plasma", - "xrefs" : [ "FMA:62970" ] + "pred" : "hasExactSynonym", + "val" : "future prosencephalon" }, { "pred" : "hasExactSynonym", - "val" : "blood plasm" + "val" : "presumptive forebrain", + "xrefs" : [ "ZFA:0000062" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of blood plasma" + "val" : "presumptive prosencephalon", + "xrefs" : [ "TAO:0000062" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "prosencephalon", + "xrefs" : [ "EHDAA2:0000661" ] } ], "xrefs" : [ { - "val" : "BTO:0000131" - }, { - "val" : "CALOHA:TS-0800" - }, { - "val" : "EFO:0001905" - }, { - "val" : "EMAPA:35690" - }, { - "val" : "FMA:62970" - }, { - "val" : "GAID:1178" + "val" : "BAMS:Pros" }, { - "val" : "MA:0002501" + "val" : "EFO:0003423" }, { - "val" : "MAT:0000052" + "val" : "EHDAA2:0000661" }, { - "val" : "MESH:D010949" + "val" : "EHDAA:2643" }, { - "val" : "MIAA:0000052" + "val" : "EMAPA:16640" }, { - "val" : "NCIT:C13356" + "val" : "TAO:0000062" }, { - "val" : "UMLS:C0032105" + "val" : "Wikipedia:Prosencephalon" }, { - "val" : "Wikipedia:Blood_plasma" + "val" : "ZFA:0000062" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "lbl" : "blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006241", + "lbl" : "future spinal cord", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A vessel through which blood circulates in the body.", - "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "vascular element", - "xrefs" : [ "EMAPA:35993" ] + "pred" : "hasExactSynonym", + "val" : "presumptive spinal cord", + "xrefs" : [ "ZFA:0000417" ] }, { "pred" : "hasExactSynonym", - "val" : "region of vascular tree organ", - "xrefs" : [ "FMA:50722" ] + "val" : "presumptive spinal cord neural keel", + "xrefs" : [ "TAO:0000417" ] }, { "pred" : "hasExactSynonym", - "val" : "vascular tree organ region", - "xrefs" : [ "FMA:50722" ] + "val" : "presumptive spinal cord neural plate", + "xrefs" : [ "TAO:0000417" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "vas sanguineum", - "xrefs" : [ "Wikipedia:Blood_vessel" ] + "pred" : "hasExactSynonym", + "val" : "presumptive spinal cord neural rod", + "xrefs" : [ "TAO:0000417" ] } ], "xrefs" : [ { - "val" : "AAO:0011004" - }, { - "val" : "AEO:0000207" - }, { - "val" : "BTO:0001102" - }, { - "val" : "CALOHA:TS-0080" - }, { - "val" : "EFO:0000817" + "val" : "EFO:0003438" }, { - "val" : "EHDAA2:0003252" + "val" : "EHDAA2:0000674" }, { - "val" : "EHDAA:240" + "val" : "EHDAA:898" }, { - "val" : "EMAPA:32743" + "val" : "EMAPA:16092" }, { - "val" : "EMAPA:35993" + "val" : "EMAPA:16755" }, { - "val" : "FMA:50722" + "val" : "TAO:0000417" }, { - "val" : "FMA:63183" + "val" : "ZFA:0000417" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", + "lbl" : "notochordal plate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", + "xrefs" : [ "VHOG:0001212" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], + "xrefs" : [ { + "val" : "EHDAA2:0001278" }, { - "val" : "GAID:169" + "val" : "EHDAA:264" }, { - "val" : "MA:0000060" + "val" : "EMAPA:16101" }, { - "val" : "MAT:0000393" + "val" : "NCIT:C34231" }, { - "val" : "MESH:D001808" + "val" : "UMLS:C1518429" }, { - "val" : "NCIT:C12679" + "val" : "VHOG:0001212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ordering; awaiting confirmation from JB" }, { - "val" : "NLXANAT:090901" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", + "lbl" : "notochordal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", + "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] + }, + "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "chordamesoderm" }, { - "val" : "SCTID:361097006" + "pred" : "hasRelatedSynonym", + "val" : "presumptive notochord" + } ], + "xrefs" : [ { + "val" : "EHDAA2:0001279" }, { - "val" : "TAO:0002137" + "val" : "EHDAA:224" }, { - "val" : "UMLS:C0005847" + "val" : "EMAPA:16102" }, { - "val" : "VHOG:0001250" + "val" : "FMA:293135" }, { - "val" : "Wikipedia:Blood_vessel" + "val" : "NCIT:C34232" }, { - "val" : "XAO:0001011" + "val" : "UMLS:C1518430" }, { - "val" : "ZFA:0005314" + "val" : "VHOG:0001213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001985", - "lbl" : "corneal endothelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006311", + "lbl" : "chamber of eyeball", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].", - "xrefs" : [ "Wikipedia:Corneal_endothelium" ] + "val" : "A segment of the eyeball that is filled with refractive media.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "cornea endothelium", - "xrefs" : [ "OBOL:automatic" ] + "val" : "eye chamber", + "xrefs" : [ "MA:0002459" ] }, { "pred" : "hasExactSynonym", - "val" : "endothelium of cornea", - "xrefs" : [ "OBOL:automatic" ] + "val" : "eyeball chamber", + "xrefs" : [ "FMA:58071" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "epithelium posterius corneae", - "xrefs" : [ "Wikipedia:Corneal_endothelium" ] + "val" : "chamber of eye", + "xrefs" : [ "BTO:0002085" ] } ], "xrefs" : [ { - "val" : "CALOHA:TS-0172" - }, { - "val" : "EMAPA:35935" - }, { - "val" : "FMA:63882" - }, { - "val" : "GAID:891" - }, { - "val" : "MA:0001242" - }, { - "val" : "MESH:D004728" + "val" : "BTO:0002085" }, { - "val" : "NCIT:C12707" + "val" : "EMAPA:37529" }, { - "val" : "SCTID:368827009" + "val" : "FMA:58071" }, { - "val" : "TAO:0002186" + "val" : "MA:0002459" }, { - "val" : "UMLS:C0014259" + "val" : "NCIT:C32301" }, { - "val" : "Wikipedia:Corneal_endothelium" + "val" : "SCTID:280540004" }, { - "val" : "ZFA:0001687" + "val" : "UMLS:C0459556" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "lbl" : "endothelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006312", + "lbl" : "ocular refractive media", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].", - "xrefs" : [ "FMA:63916", "MESH:A10.272.491", "https://github.com/obophenotype/uberon/issues/225" ] + "val" : "Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "xrefs" : [ { - "val" : "BTO:0000393" - }, { - "val" : "CALOHA:TS-0278" - }, { - "val" : "EFO:0002548" - }, { - "val" : "FMA:63916" - }, { - "val" : "GAID:520" - }, { - "val" : "MESH:D004727" - }, { - "val" : "NCIT:C12481" - }, { - "val" : "SCTID:27168002" - }, { - "val" : "UMLS:C0014257" - }, { - "val" : "galen:Endothelium" + "val" : "MA:0001911" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002020", - "lbl" : "gray matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006314", + "lbl" : "bodily fluid", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.", - "xrefs" : [ "Wikipedia:Gray_matter", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", + "xrefs" : [ "MESH:A12.207", "Wikipedia:Body_fluid" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gray matter" + "pred" : "hasBroadSynonym", + "val" : "fluid" }, { "pred" : "hasExactSynonym", - "val" : "gray matter of neuraxis", - "xrefs" : [ "FMA:67242" ] + "val" : "body fluid", + "xrefs" : [ "GAID:266" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:20" }, { - "pred" : "hasExactSynonym", - "val" : "grey matter" + "val" : "EMAPA:37441" }, { - 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Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracolumbar region" - }, { - "pred" : "hasExactSynonym", - "val" : "torso" - }, { - "pred" : "hasExactSynonym", - "val" : "trunk region", - "xrefs" : [ "XAO:0000054" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Rumpf", - "xrefs" : [ "BTO:0001493" ] - } ], + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "AAO:0010339" - }, { - "val" : "BILA:0000116" - }, { - "val" : "BTO:0001493" - }, { - "val" : "CALOHA:TS-1071" - }, { - "val" : "EFO:0000966" - }, { - "val" : "EMAPA:31857" - }, { - "val" : "FMA:7181" - }, { - "val" : "MA:0000004" - }, { - "val" : "MAT:0000296" - }, { - "val" : "MIAA:0000296" - }, { - "val" : "NCIT:C33816" - }, { - "val" : "SCTID:262225004" - }, { - "val" : "TAO:0001115" - }, { - "val" : "UMLS:C0460005" + "val" : "BILA:0000010" }, { - "val" : "Wikipedia:Torso" + "val" : "CARO:0001002" }, { - "val" : "XAO:0000054" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "XAO:0003025" + "val" : "FMA:24137" }, { - "val" : "ZFA:0001115" + "val" : "NCIT:C34022" }, { - "val" : "galen:Trunk" + "val" : "UMLS:C1515977" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24846,87 +27737,77 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002104", - "lbl" : "visual system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "lbl" : "cardiogenic splanchnic mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The sensory system subserving the sense of vision.", - "xrefs" : [ "NIFSTD:FMAID_7191" ] + "val" : "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. 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The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.", + "xrefs" : [ "Wikipedia:Rhombencephalon" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "SpC" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cerebro-cerebellar fissure", - "xrefs" : [ "NeuroNames:22" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cerebrocerebellar fissure", - "xrefs" : [ "NeuroNames:22" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "fissura cerebro-cerebellaris", - "xrefs" : [ "NeuroNames:22" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "fissura cerebrocerebellaris", - "xrefs" : [ "NeuroNames:22" ] + "pred" : "hasExactSynonym", + "val" : "presumptive rhombencephalon", + "xrefs" : [ "ZFA:0000569" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "medulla spinalis", - "xrefs" : [ "BTO:0001279", "Wikipedia:Spinal_cord" ] + "val" : "embryonic rhombencephalon", + "xrefs" : [ "CALOHA:TS-2118" ] }, { "pred" : "hasRelatedSynonym", - "val" : "spinal cord structure", - "xrefs" : [ "ZFA:0000075" ] + "val" : "future hindbrain", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "spinal medulla", - "xrefs" : [ "BTO:0001279" ] + "val" : "rhombencephalon", + "xrefs" : [ "EHDAA2:0001630" ] } ], "xrefs" : [ { - "val" : "AAO:0010151" - }, { - "val" : "BAMS:SP" - }, { - "val" : "BAMS:Spinal" - }, { - "val" : "BIRNLEX:1709" - }, { - "val" : "BM:SpC" - }, { - "val" : "BTO:0001279" - }, { - "val" : "CALOHA:TS-0953" - }, { - "val" : "DHBA:12890" - }, { - "val" : "DMBA:17651" - }, { - "val" : "EFO:0000110" - }, { - "val" : "EHDAA2:0001255" - }, { - "val" : "EHDAA:2863" - }, { - "val" : "EMAPA:17577" - }, { - "val" : "EV:0100316" - }, { - "val" : "FMA:7647" - }, { - "val" : "GAID:695" - }, { - "val" : "MA:0000216" - }, { - "val" : "MAT:0000183" - }, { - "val" : "MESH:D013116" - }, { - "val" : "MIAA:0000183" - }, { - "val" : "NCIT:C12464" - }, { - "val" : "SCTID:180959008" + "val" : "BAMS:HB" }, { - "val" : "TAO:0000075" + "val" : "CALOHA:TS-2118" }, { - "val" : "UMLS:C0037925" + "val" : "EFO:0003440" }, { - "val" : "VHOG:0000601" + "val" : "EHDAA2:0001630" }, { - "val" : "Wikipedia:Spinal_cord" + "val" : "FMA:295640" }, { - "val" : "XAO:0000020" + "val" : "TAO:0000569" }, { - "val" : "ZFA:0000075" + "val" : "Wikipedia:Rhombencephalon" }, { - "val" : "neuronames:22" + "val" : "ZFA:0000569" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - add superclass to unify with VNC?" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "TODO - unify naming conventions" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002298", - "lbl" : "brainstem", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007281", + "lbl" : "presumptive midbrain hindbrain boundary", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].", - "xrefs" : [ "ISBN:0471888893", "MP:0005277", "Wikipedia:Brainstem", "ZFA:0001707" ] + "val" : "Embryonic structure that gives rise to the midbrain hindbrain boundary.", + "xrefs" : [ "ZFA:0001187" ] }, - "comments" : [ "'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "brain stem", - "xrefs" : [ "ABA:BS" ] + "val" : "presumptive MHB", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "truncus encephali", - "xrefs" : [ "Wikipedia:Brainstem" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory medullary lamina of pallidum", - "xrefs" : [ "NeuroNames:236" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamella pallidi incompleta", - "xrefs" : [ "NeuroNames:236" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina medullaris accessoria", - "xrefs" : [ "NeuroNames:236" ] + "val" : "presumptive midbrain-hindbrain boundary", + "xrefs" : [ "ZFA:0001187" ] + } ], + "xrefs" : [ { + "val" : "EFO:0003446" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina medullaris incompleta pallidi", - "xrefs" : [ "NeuroNames:236" ] + "val" : "TAO:0001187" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina pallidi incompleta", - "xrefs" : [ "NeuroNames:236" ] + "val" : "XAO:0004086" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "val" : "ZFA:0001187" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007282", + "lbl" : "presumptive segmental plate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A presumptive structure that has the potential to develop into a presomitic mesoderm.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "truncus encephalicus", - "xrefs" : [ "BTO:0000146" ] + "val" : "presumptive segmental plates", + "xrefs" : [ "ZFA:0000053" ] } ], "xrefs" : [ { - "val" : "BAMS:BS" - }, { - "val" : "BIRNLEX:1565" - }, { - "val" : "BTO:0000146" - }, { - "val" : "CALOHA:TS-0093" - }, { - "val" : "EFO:0001962" - }, { - "val" : "EMAPA:32678" - }, { - "val" : "EV:0100241" - }, { - "val" : "FMA:79876" - }, { - "val" : "MA:0000169" - }, { - "val" : "MBA:343" - }, { - "val" : "MESH:D001933" - }, { - "val" : "NCIT:C12441" - }, { - "val" : "SCTID:180925009" - }, { - "val" : "TAO:0002156" - }, { - "val" : "UMLS:C0006121" - }, { - "val" : "VHOG:0001457" - }, { - "val" : "Wikipedia:Brainstem" + "val" : "EFO:0003421" }, { - "val" : "ZFA:0001707" + "val" : "TAO:0000053" }, { - "val" : "neuronames:236" + "val" : "ZFA:0000053" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002316", - "lbl" : "white matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007284", + "lbl" : "presumptive neural plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.", - "xrefs" : [ "Wikipedia:White_matter", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A presumptive structure that has the potential to develop into a neural plate.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "CNS tract/commissure", - "xrefs" : [ "ZFA:0001682" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neuronal white matter", - "xrefs" : [ "AEO:0001011" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white matter of neuraxis", - "xrefs" : [ "FMA:83929" ] + "val" : "prospective neuroectoderm", + "xrefs" : [ "ZFA:0000063" ] }, { "pred" : "hasExactSynonym", - "val" : "white substance" - }, { - "pred" : "hasRelatedSynonym", - "val" : "CNS tracts and commissures", - "xrefs" : [ "TAO:0000145" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "CNS white matter", - "xrefs" : [ "TAO:0002143" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "substantia alba", - "xrefs" : [ "Wikipedia:White_matter" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "white mater", - "xrefs" : [ "VHOG:0001764" ] + "val" : "prospective vegetal ectoderm", + "xrefs" : [ "ZFA:0000063" ] } ], "xrefs" : [ { - "val" : "AEO:0000139" - }, { - "val" : "AEO:0001011" - }, { - "val" : "EMAPA:35927" - }, { - "val" : "FMA:83929" - }, { - "val" : "HBA:9218" - }, { - "val" : "MA:0001135" - }, { - "val" : "NCIT:C33892" - }, { - "val" : "NLX:412" - }, { - "val" : "NLXANAT:101177" - }, { - "val" : "PBA:294022044" - }, { - "val" : "TAO:0000145" + "val" : "EFO:0003424" }, { - "val" : "TAO:0002142" + "val" : "TAO:0000063" }, { - "val" : "TAO:0002143" + "val" : "ZFA:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging" }, { - "val" : "UMLS:C0682708" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007285", + "lbl" : "presumptive paraxial mesoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The part of the blastula that has the potential to develop into a paraxial mesoderm.", + "xrefs" : [ "UBERON:cjm", "https://github.com/obophenotype/uberon/issues/1277" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "future paraxial mesenchyme", + "xrefs" : [ "UBERON:cjm" ] }, { - "val" : "VHOG:0001764" + "pred" : "hasExactSynonym", + "val" : "future paraxial mesoderm" + } ], + "xrefs" : [ { + "val" : "EFO:0003443" }, { - "val" : "Wikipedia:White_matter" + "val" : "TAO:0000591" }, { - "val" : "ZFA:0001682" + "val" : "XAO:0004134" }, { - "val" : "neuronames:2870" + "val" : "ZFA:0000591" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", - "lbl" : "coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007418", + "lbl" : "neural decussation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.", - "xrefs" : [ "BTO:0001707" ] + "val" : "Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6).", + "xrefs" : [ "NLX:144064" ] }, - "comments" : [ "EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo" ], "synonyms" : [ { "pred" : "hasBroadSynonym", - "val" : "body cavity", - "xrefs" : [ "BTO:0001707" ] + "val" : "chiasm" }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity", - "xrefs" : [ "EHDAA2:0000267" ] + "pred" : "hasBroadSynonym", + "val" : "chiasma" }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity lumen", - "xrefs" : [ "EHDAA2:0000267" ] + "pred" : "hasBroadSynonym", + "val" : "decussation" }, { "pred" : "hasExactSynonym", - "val" : "main body cavity" + "val" : "decussation of neuraxis", + "xrefs" : [ "FMA:83858" ] }, { "pred" : "hasExactSynonym", - "val" : "space of body compartment", - "xrefs" : [ "FMA:85006" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "ventral body cavity", - "xrefs" : [ "NCBITaxon:7742" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "celom", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "coelom" + "val" : "neuraxis chiasm" }, { - "pred" : "hasRelatedSynonym", - "val" : "coelome", - "xrefs" : [ "BTO:0001707" ] + "pred" : "hasExactSynonym", + "val" : "neuraxis chiasma" }, { - "pred" : "hasRelatedSynonym", - "val" : "hemocoel", - "xrefs" : [ "FBbt:00005060" ] + "pred" : "hasExactSynonym", + "val" : "neuraxis decussation", + "xrefs" : [ "FMA:83858" ] } ], "xrefs" : [ { - "val" : "AEO:0000186" - }, { - "val" : "BTO:0001707" - }, { - "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" - }, { - "val" : "FMA:85006" - }, { - "val" : "NCIT:C25444" - }, { - "val" : "RETIRED_EHDAA2:0003186" - }, { - "val" : "SCTID:361348008" - }, { - "val" : "TAO:0001438" + "val" : "FMA:83858" }, { - "val" : "UMLS:C0333343" + "val" : "NCIT:C28351" }, { - "val" : "ZFA:0001438" + "val" : "NLX:144064" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007425", + "lbl" : "decussation of diencephalon", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A neural decussation that is part of a diencephalon.", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "diencephalon decussation", + "xrefs" : [ "FMA:62446" ] + } ], + "xrefs" : [ { + "val" : "FMA:62446" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007500", + "lbl" : "epithelial tube open at both ends", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelial tube open at both ends that allows fluid flow.", + "xrefs" : [ "AEO:JB", "UBERONREF:0000001" ] + }, + "xrefs" : [ { + "val" : "AEO_RETIRED:0000116" }, { - "val" : "galen:BodyCavity" + "val" : "RETIRED_EHDAA2:0003116" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "lbl" : "notochord", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007503", + "lbl" : "epithelial vesicle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A flexible rod-shaped body found in embryos of all chordates. 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In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" + "pred" : "hasBroadSynonym", + "val" : "field" }, { "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] + "val" : "developmental field" }, { - "pred" : "hasExactSynonym", - "val" : "textus muscularis" + "pred" : "hasRelatedSynonym", + "val" : "future organ" + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ field" } ], "xrefs" : [ { - "val" : "AAO:0000306" - }, { - "val" : "AEO:0000122" - }, { - "val" : "CALOHA:TS-0642" - }, { - "val" : "EHDAA2:0003122" - }, { - "val" : "EMAPA:32715" - }, { - "val" : "FMA:9641" - }, { - "val" : "MA:0002437" - }, { - "val" : "MESH:D009132" - }, { - "val" : "NCIT:C12435" + "val" : "AEO:0000170" }, { - "val" : "SCTID:91727004" + "val" : "EFO:0001649" }, { - "val" : "UMLS:C2328219" + "val" : "EHDAA2:0003170" }, { - "val" : "Wikipedia:Muscle_tissue" + "val" : "FBbt:00005426" }, { - "val" : "galen:MuscleTissue" + "val" : "Wikipedia:Anlage_(biology)" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -25997,142 +28405,63 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007702", + "lbl" : "tract of brain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "An axon tract that is part of a brain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "haematological system" - }, { - "pred" : "hasExactSynonym", - "val" : "haemopoietic system" - }, { - "pred" : "hasExactSynonym", - "val" : "organa haemopoietica" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Blutbildungssystem", - "xrefs" : [ "BTO:0000570" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "haematopoietic system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematological system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematolymphoid system" + "val" : "brain tract", + "xrefs" : [ "FMA:83848" ] }, { "pred" : "hasRelatedSynonym", - "val" : "hemopoietic system" + "val" : "landmark tracts", + "xrefs" : [ "DMBA:tracts" ] } ], "xrefs" : [ { - "val" : "AAO:0011002" - }, { - "val" : "BTO:0000570" - }, { - "val" : "CALOHA:TS-0449" - }, { - "val" : "EFO:0000798" - }, { - "val" : "EMAPA:35402" - }, { - "val" : "EV:0100045" - }, { - "val" : "FMA:9667" - }, { - "val" : "GAID:1008" - }, { - "val" : "MA:0002434" - }, { - "val" : "MAT:0000022" - }, { - "val" : "MESH:D006413" - }, { - "val" : "MIAA:0000022" - }, { - "val" : "NCIT:C12909" - }, { - "val" : "SCTID:362587009" - }, { - "val" : "TAO:0005023" - }, { - "val" : "UMLS:C0018957" - }, { - "val" : "VHOG:0001624" - }, { - "val" : "Wikipedia:Haematopoiesis" - }, { - "val" : "XAO:0000122" - }, { - "val" : "ZFA:0005023" + "val" : "FMA:83848" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002506", - "lbl" : "iris epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007798", + "lbl" : "vascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelium that is part of a iris [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Anatomical system that consists of all blood and lymph vessels.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial tissue of iris", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of iris", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium pigmentosum (iris)", - "xrefs" : [ "FMA:58517" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "epithelium pigmentosum iridis", - "xrefs" : [ "FMA:58517", "FMA:TA" ] + "xrefs" : [ { + "val" : "BTO:0001085" }, { - "pred" : "hasExactSynonym", - "val" : "iris epithelial tissue", - "xrefs" : [ "OBOL:automatic" ] + "val" : "CALOHA:TS-2053" }, { - "pred" : "hasExactSynonym", - "val" : "iris epithelium", - "xrefs" : [ "FMA:58517" ] + "val" : "EHDAA2:0004520" }, { - "pred" : "hasExactSynonym", - "val" : "pigmented epithelium of iris", - "xrefs" : [ "FMA:58517" ] + "val" : "EMAPA:35905" }, { - "pred" : "hasRelatedSynonym", - "val" : "iris pigmented epithelium", - "xrefs" : [ "MA:0002826" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35447" + "val" : "MA:0002718" }, { - "val" : "FMA:58517" + "val" : "NCIT:C33854" }, { - "val" : "MA:0002826" + "val" : "UMLS:C0489903" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with vasculature" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -26141,134 +28470,105 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", - "lbl" : "epiblast (generic)", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007811", + "lbl" : "craniocervical region", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", - "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] + "val" : "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epiblast", - "xrefs" : [ "VHOG:0000243" ] + "pred" : "hasRelatedSynonym", + "val" : "cephalic area", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] }, { "pred" : "hasRelatedSynonym", - "val" : "blastocyst" + "val" : "cephalic part of animal", + "xrefs" : [ "Wikipedia:Head" ] }, { "pred" : "hasRelatedSynonym", - "val" : "ectoblast", - "xrefs" : [ "MP:0003886" ] + "val" : "cephalic region", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "epiblastus", - "xrefs" : [ "Wikipedia:Epiblast" ] + "val" : "head and neck", + "xrefs" : [ "FMA:280881" ] }, { "pred" : "hasRelatedSynonym", - "val" : "primitive ectoderm", - "xrefs" : [ "VHOG:0000243" ] + "val" : "head or neck" } ], "xrefs" : [ { - "val" : "BTO:0004593" + "val" : "CALOHA:TS-2356" }, { - "val" : "FMA:296704" + "val" : "EV:0100009" }, { - "val" : "MAT:0000067" + "val" : "FMA:280881" }, { - "val" : "MIAA:0000067" + "val" : "MA:0000006" }, { - "val" : "VHOG:0000243" + "val" : "NCIT:C12418" }, { - "val" : "Wikipedia:Epiblast" + "val" : "SCTID:361355005" + }, { + "val" : "UMLS:C0460004" + }, { + "val" : "WikipediaCategory:Head_and_neck" + }, { + "val" : "galen:HeadAndNeck" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002546", - "lbl" : "cranial placode", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", + "lbl" : "entire embryonic mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.", - "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK53175/", "https://github.com/obophenotype/uberon/issues/135", "https://github.com/seger/aao/issues/4", "https://orcid.org/0000-0002-6601-2165", "https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/" ] + "val" : "Sum total of mesenchyme in the embryo.", + "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", - "pred" : "hasBroadSynonym", - "val" : "ectodermal placode", - "xrefs" : [ "FMA:293966", "PMID:22512454" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "placode", - "xrefs" : [ "Wikipedia:Placode" ] - }, { - "pred" : "hasExactSynonym", - "val" : "ectodermal cranial placode", - "xrefs" : [ "UBERON:cjm" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "cranial placodes", - "xrefs" : [ "XAO:0000305" ] - } ], "xrefs" : [ { - "val" : "AAO:0010466" - }, { - "val" : "EFO:0001650" - }, { - "val" : "MAT:0000369" + "val" : "EHDAA2:0001113" }, { - "val" : "MIAA:0000369" + "val" : "EHDAA:177" }, { - "val" : "XAO:0000305" + "val" : "EMAPA:16097" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Do not merge with neurogenic placode" + "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", + "lbl" : "subdivision of trunk", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" + "pred" : "hasExactSynonym", + "val" : "region of trunk", + "xrefs" : [ "FMA:25054" ] + }, { + "pred" : "hasExactSynonym", + "val" : "trunk subdivision", + "xrefs" : [ "FMA:25054" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" - }, { - "val" : "NCIT:C34007" + "val" : "FMA:25054" }, { - "val" : "galen:Cavity" + "val" : "SCTID:22943007" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26276,154 +28576,127 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002616", - "lbl" : "regional part of brain", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009581", + "lbl" : "midbrain mantle layer", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.", - "xrefs" : [ "BIRNLEX:1167" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "anatomical structure of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "biological structure of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "brain anatomical structure", - "xrefs" : [ "OBOL:automatic" ] + "val" : "mantle layer lateral wall midbrain", + "xrefs" : [ "VHOG:0000910" ] }, { "pred" : "hasExactSynonym", - "val" : "brain biological structure", - "xrefs" : [ "OBOL:automatic" ] + "val" : "midbrain lateral wall mantle layer" }, { - "pred" : "hasExactSynonym", - "val" : "brain part" + "pred" : "hasRelatedSynonym", + "val" : "mantle layer lateral wall mesencephalon", + "xrefs" : [ "VHOG:0000910" ] + } ], + "xrefs" : [ { + "val" : "EHDAA2:0001172" }, { - "pred" : "hasExactSynonym", - "val" : "neuraxis segment", - "xrefs" : [ "FMA:55676" ] + "val" : "EMAPA:16977" }, { + "val" : "VHOG:0000910" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009615", + "lbl" : "midbrain hindbrain boundary neural plate", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neuroanatomical region" + "val" : "MHB neural plate", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "segment of brain", - "xrefs" : [ "BIRNLEX:1167" ] + "val" : "midbrain-hindbrain boundary neural plate", + "xrefs" : [ "ZFA:0007044" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1167" - }, { - "val" : "FMA:55676" - }, { - "val" : "NCIT:C13031" - }, { - "val" : "SCTID:384763002" + "val" : "TAO:0007044" }, { - "val" : "UMLS:C0445620" + "val" : "ZFA:0007044" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - developmental relationships for lines" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003052", - "lbl" : "midbrain-hindbrain boundary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009616", + "lbl" : "presumptive midbrain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.", - "xrefs" : [ "GO:0021555" ] + "val" : "A presumptive structure that has the potential to develop into a midbrain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "MHB" - }, { - "pred" : "hasExactSynonym", - "val" : "mid-hindbrain boundary" - }, { - "pred" : "hasExactSynonym", - "val" : "mid-hindbrain junction" - }, { - "pred" : "hasExactSynonym", - "val" : "midbrain hindbrain boundary" - }, { - "pred" : "hasRelatedSynonym", - "val" : "isthmic organizer territory", - "xrefs" : [ "XAO:0000016" ] + "val" : "presumptive mesencephalon", + "xrefs" : [ "ZFA:0000148" ] }, { "pred" : "hasRelatedSynonym", - "val" : "isthmo-cerebellar region", - "xrefs" : [ "VHOG:0000649" ] + "val" : "early midbrain", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "isthmus" + "val" : "future midbrain", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "isthmus/MHB", - "xrefs" : [ "Geisha:syn", "NCBITaxon:8782" ] + "val" : "mesencephalon", + "xrefs" : [ "EHDAA2:0000615" ] } ], "xrefs" : [ { - "val" : "AAO:0011064" - }, { - "val" : "DMBA:16810" - }, { - "val" : "EHDAA2:0004395" - }, { - "val" : "EHDAA:5789" - }, { - "val" : "EMAPA:32857" + "val" : "BAMS:MES" }, { - "val" : "NCIT:C93172" + "val" : "EFO:0003432" }, { - "val" : "TAO:0000042" + "val" : "EHDAA2:0000615" }, { - "val" : "VHOG:0000649" + "val" : "EMAPA:16140" }, { - "val" : "XAO:0000016" + "val" : "TAO:0000148" }, { - "val" : "ZFA:0000042" + "val" : "Wikipedia:Mesencephalon" }, { - "val" : "neuronames:2076" + "val" : "ZFA:0000148" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding class for organizer. Consider adding separate class for isthmus as a structure" + "val" : "TODO - unify naming conventions" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003056", - "lbl" : "pre-chordal neural plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", + "lbl" : "trunk paraxial mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "The portion of neural plate anterior to the mid-hindbrain junction.", - "xrefs" : [ "XB:curator" ] - }, "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "trunk and cervical paraxial mesenchyme", + "xrefs" : [ "EHDAA2:0002094" ] + }, { "pred" : "hasRelatedSynonym", - "val" : "anterior neural plate" + "val" : "trunk paraxial mesenchyme", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] } ], "xrefs" : [ { - "val" : "AAO:0011084" - }, { - "val" : "TAO:0007016" - }, { - "val" : "VHOG:0001200" - }, { - "val" : "XAO:0000045" - }, { - "val" : "ZFA:0007016" + "val" : "EHDAA2:0002094" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26431,26 +28704,22 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003057", - "lbl" : "chordal neural plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "lbl" : "anterior lateral plate mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "The portion of neural plate posterior to the mid-hindbrain junction.", - "xrefs" : [ "XB:curator" ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "posterior neural plate" + "pred" : "hasExactSynonym", + "val" : "ALPM", + "xrefs" : [ "ZFA:0005041" ] } ], "xrefs" : [ { - "val" : "TAO:0007017" - }, { - "val" : "VHOG:0001201" + "val" : "EFO:0003704" }, { - "val" : "XAO:0000046" + "val" : "TAO:0005041" }, { - "val" : "ZFA:0007017" + "val" : "ZFA:0005041" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26458,56 +28727,40 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009891", + "lbl" : "facial mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "Mesenchyme that is part of a developing face.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segmental plate" + "val" : "face mesenchyme" }, { "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] + "val" : "mesenchyme of face" } ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" + "val" : "EMAPA:35337" }, { - "val" : "XAO:0000057" + "val" : "FMA:302884" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009920", + "lbl" : "optic neural crest", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EHDAA2:0001315" }, { - "val" : "ZFA:0000279" + "val" : "EHDAA:1122" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26515,219 +28768,150 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", - "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ventral lateral plate mesoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "blood islands" - }, { - "pred" : "hasRelatedSynonym", - "val" : "VBI" - }, { - "pred" : "hasRelatedSynonym", - "val" : "caudal hematopoietic tissue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior ICM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior blood island" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral blood island" + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { - "val" : "AAO:0011006" - }, { - "val" : "EFO:0003489" - }, { - "val" : "EHDAA:207" - }, { - "val" : "NCIT:C34113" - }, { - "val" : "TAO:0000094" - }, { - "val" : "TE:E5.11.2.0.0.0.4" - }, { - "val" : "UMLS:C1511224" + "val" : "CARO:0010000" }, { - "val" : "VHOG:0000085" + "val" : "FBbt:00100313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "Wikipedia:Blood_island_of_umbilical_vesicle" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "XAO:0000067" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "ZFA:0000094" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "lbl" : "axial mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010096", + "lbl" : "future myelencephalon", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.", - "xrefs" : [ "GO:0048318", "Wikipedia:Chordamesoderm" ] + "val" : "A developing anatomical structure that has the potential to develop into a myelencephalon.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm", - "xrefs" : [ "Wikipedia:Chordamesoderm" ] - } ], "xrefs" : [ { - "val" : "AAO:0011017" - }, { - "val" : "EFO:0003647" - }, { - "val" : "TAO:0001204" - }, { - "val" : "VHOG:0000107" - }, { - "val" : "Wikipedia:Chordamesoderm" - }, { - "val" : "XAO:0000205" - }, { - "val" : "ZFA:0001204" + "val" : "EHDAA2:0000640" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010199", + "lbl" : "bona-fide anatomical boundary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical boundary that corresponds to some physical discontinuity.", + "xrefs" : [ "CARO:0001004" ] + }, + "comments" : [ "One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "CARO:0001004" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003071", - "lbl" : "eye primordium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010230", + "lbl" : "eyeball of camera-type eye", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. 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Excludes joints.", + "xrefs" : [ "UBERONREF:0000003", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cardiac field", - "xrefs" : [ "ZFA:0000028" ] + "pred" : "hasExactSynonym", + "val" : "skeletal subdivision", + "xrefs" : [ "VSAO:0000042" ] }, { "pred" : "hasRelatedSynonym", - "val" : "fused heart primordium" + "val" : "subdivision of skeleton (in vivo)", + "xrefs" : [ "FMA:23879" ] } ], "xrefs" : [ { - "val" : "AAO:0011044" - }, { - "val" : "BTO:0001887" - }, { - "val" : "NCIT:C34276" - }, { - "val" : "TAO:0000028" - }, { - "val" : "UMLS:C1514450" + "val" : "FMA:23879" }, { - "val" : "XAO:0000336" + "val" : "SCTID:129140006" }, { - "val" : "ZFA:0000028" + "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "should probably be merged with heart rudiment." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "lbl" : "sclerotome", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011137", + "lbl" : "axial skeletal system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].", - "xrefs" : [ "Wikipedia:Sclerotome", "XB:curator", "https://github.com/obophenotype/uberon/issues/316" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "sclerotomes", - "xrefs" : [ "TAO:0001080" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "sclerotomus", - "xrefs" : [ "Wikipedia:Sclerotome" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010571" - }, { - "val" : "AEO:0000212" - }, { - "val" : "EHDAA2:0003439" - }, { - "val" : "EMAPA:31159" - }, { - "val" : "FMA:295652" - }, { - "val" : "NCIT:C34287" - }, { - "val" : "TAO:0001080" - }, { - "val" : "UMLS:C0183176" - }, { - "val" : "VHOG:0000680" - }, { - "val" : "Wikipedia:Sclerotome" - }, { - "val" : "XAO:0000397" - }, { - "val" : "ZFA:0001080" + "val" : "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "xrefs" : [ { + "val" : "FMA:7483" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003098", - "lbl" : "optic stalk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011138", + "lbl" : "postcranial axial skeletal system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain.", - "xrefs" : [ "ISBN:0-914294-08-3", "MP:0004268" ] + "val" : "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/44", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "optic stalks", - "xrefs" : [ "ZFA:0000137" ] + "pred" : "hasBroadSynonym", + "val" : "axial skeletal system", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "pedunculus opticus", - "xrefs" : [ "Wikipedia:Optic_stalk" ] + "pred" : "hasExactSynonym", + "val" : "post-cranial axial skeletal system" } ], "xrefs" : [ { - "val" : "AAO:0011077" - }, { - "val" : "EHDAA2:0001318" - }, { - "val" : "EHDAA:3816" - }, { - "val" : "EMAPA:16678" - }, { - "val" : "NCIT:C34235" - }, { - "val" : "SCTID:308788004" - }, { - "val" : "TAO:0000137" - }, { - "val" : "UMLS:C0231107" - }, { - "val" : "VHOG:0000223" - }, { - "val" : "Wikipedia:Optic_stalk" - }, { - "val" : "XAO:0000475" - }, { - "val" : "ZFA:0000137" + "val" : "FMA:302077" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003099", - "lbl" : "cranial neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011215", + "lbl" : "central nervous system cell part cluster", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.", - "xrefs" : [ "MGI:anna" ] + "val" : "A multi cell part structure that is part of a central nervous system.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "CNC", - "xrefs" : [ "XAO:0001001" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cephalic neural crest", - "xrefs" : [ "EMAPA:16091" ] - }, { "pred" : "hasExactSynonym", - "val" : "cranial NCC population" + "val" : "cell part cluster of neuraxis", + "xrefs" : [ "FMA:83143" ] }, { "pred" : "hasExactSynonym", - "val" : "head NCC population" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "crista neuralis cranialis", - "xrefs" : [ "Wikipedia:Cranial_neural_crest" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "head crest" - }, { - "pred" : "hasRelatedSynonym", - "val" : "head neural crest" + "val" : "neuraxis layer", + "xrefs" : [ "FMA:83143" ] } ], "xrefs" : [ { - "val" : "AAO:0010580" - }, { - "val" : "EFO:0003645" - }, { - "val" : "EHDAA2:0004420" - }, { - "val" : "EMAPA:16091" - }, { - "val" : "TAO:0001194" - }, { - "val" : "VHOG:0000063" - }, { - "val" : "Wikipedia:Cranial_neural_crest" - }, { - "val" : "XAO:0001001" - }, { - "val" : "ZFA:0001194" + "val" : "FMA:83143" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27237,275 +29225,161 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", - "lbl" : "compound organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011216", + "lbl" : "organ system subdivision", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", - "xrefs" : [ "CARO:0000024" ] + "val" : "A subdivision of an anatomical system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "organ" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "AAO:0010015" - }, { - "val" : "AEO:0000024" - }, { - "val" : "BILA:0000024" - }, { - "val" : "CARO:0000024" - }, { - "val" : "EHDAA2:0003024" - }, { - "val" : "HAO:0000024" + "val" : "FBbt:00007330" }, { - "val" : "TADS:0000598" + "val" : "FMA:67509" }, { - "val" : "TAO:0000496" + "val" : "SCTID:91690000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "TGMA:0001837" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "VHOG:0001723" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "XAO:0003041" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "ZFA:0000496" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "lbl" : "mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011222", + "lbl" : "intra-ocular muscle", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.", - "xrefs" : [ "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up", "https://en.wikipedia.org/wiki/Mesenchyme", "https://github.com/obophenotype/uberon/issues/1641" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "mesenchymal tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "mesenchyme tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of mesenchymal tissue" + "val" : "intrinsic muscle of eyeball" }, { "pred" : "hasExactSynonym", - "val" : "portion of mesenchyme tissue" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesenchyma", - "xrefs" : [ "Wikipedia:Mesenchyme" ] + "val" : "intrinsic ocular muscle", + "xrefs" : [ "EMAPA:18808" ] } ], "xrefs" : [ { - "val" : "AAO:0010427" - }, { - "val" : "AEO:0000145" - }, { - "val" : "BTO:0001393" - }, { - "val" : "CALOHA:TS-0620" - }, { - "val" : "EHDAA2:0003145" - }, { - "val" : "EV:0100007" - }, { - "val" : "NCIT:C13301" - }, { - "val" : "TAO:0000393" - }, { - "val" : "UMLS:C0162415" - }, { - "val" : "VHOG:0000170" - }, { - "val" : "Wikipedia:Mesenchyme" + "val" : "AAO:0010038" }, { - "val" : "XAO:0003046" + "val" : "EMAPA:18808" }, { - "val" : "ZFA:0000393" + "val" : "FMA:49150" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003314", - "lbl" : "eye mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011585", + "lbl" : "cell condensation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Mesenchyme that is part of a developing camera-type eye.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000006", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of eye", - "xrefs" : [ "OBOL:automatic" ] - } ], "xrefs" : [ { - "val" : "EHDAA2:0000485" - }, { - "val" : "EHDAA:2910" - }, { - "val" : "EMAPA:16673" + "val" : "VSAO:0000006" }, { - "val" : "VHOG:0001084" + "val" : "XAO:0004021" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - change mesenchyme relationships to precursor_of" + "val" : "consider obsoleting, coordinate with VSAO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003386", - "lbl" : "smooth muscle of eye", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011591", + "lbl" : "tract of diencephalon", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi.", - "xrefs" : [ "MGI:cwg", "MP:0005247" ] + "val" : "An axon tract that is part of a diencephalon.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "ocular smooth muscle", - "xrefs" : [ "MA:0001268" ] + "val" : "diencephalon tract", + "xrefs" : [ "FMA:62447" ] } ], "xrefs" : [ { - "val" : "EMAPA:18807" - }, { - "val" : "MA:0001268" + "val" : "FMA:62447" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003544", - "lbl" : "brain white matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011676", + "lbl" : "subdivision of organism along main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.", - "xrefs" : [ "MP:0008026" ] + "val" : "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "brain white matter of neuraxis", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "brain white substance", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white matter of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white matter of neuraxis of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white substance of brain", - "xrefs" : [ "OBOL:automatic" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35187" - }, { - "val" : "MA:0000820" + "val" : "axial subdivision of organism" }, { - "val" : "NCIT:C49334" + "pred" : "hasRelatedSynonym", + "val" : "body segment" }, { - "val" : "UMLS:C1706995" + "pred" : "hasRelatedSynonym", + "val" : "main body segment" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003566", - "lbl" : "head connective tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", + "lbl" : "embryonic cardiovascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A portion of connective tissue that is part of a head [Automatically generated definition].", + "val" : "A cardiovascular system that is part of a conceptus.", "xrefs" : [ "OBOL:automatic" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "adult head connective tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "adult head portion of connective tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "adult head textus connectivus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "connective tissue of adult head", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "connective tissue of head", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "head portion of connective tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "head textus connectivus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue of adult head", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue of head", - "xrefs" : [ "OBOL:automatic" ] + "val" : "conceptus cardiovascular system" }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus of adult head", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "embryonic circulatory system" }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus of head", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "fetal circulatory system" } ], "xrefs" : [ { - "val" : "MA:0000577" + "val" : "EHDAA2:0000216" + }, { + "val" : "FMA:305965" + }, { + "val" : "NCIT:C34148" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27513,141 +29387,64 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003714", - "lbl" : "neural tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011814", + "lbl" : "non-neurogenic ectodermal placode", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.", - "xrefs" : [ "FMA:9642" ] + "val" : "Ectodermal placode that does not develop into a component of the nervous system.", + "xrefs" : [ "PMID:11523831", "http://orcid.org/0000-0002-6601-2165" ] }, - 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"xrefs" : [ "OBOL:automatic" ] + "val" : "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.", + "xrefs" : [ "FMA:20107" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cavity of neural tube", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "lumen of neural tube", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neural tube neural lumen", - "xrefs" : [ "EHDAA2:0001269" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "prosencoel" - }, { - "pred" : "hasRelatedSynonym", - "val" : "central lumen" - }, { - "pred" : "hasRelatedSynonym", - "val" : "neural lumen", - "xrefs" : [ "EHDAA:2889" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neurocoel", - "xrefs" : [ "VHOG:0001119" ] - } ], "xrefs" : [ { - "val" : "AAO:0011073" - }, { - "val" : "EHDAA2:0001269" - }, { - "val" : "EHDAA:2889" - }, { - "val" : "EHDAA:914" - }, { - "val" : "EMAPA:16167" - }, { - "val" : "VHOG:0001119" - }, { - "val" : "XAO:0000252" + "val" : "FMA:20107" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005713" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003849", - "lbl" : "mesencephalic neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011825", + "lbl" : "loose connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a midbrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.", + "xrefs" : [ "FMA:19783" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "mesencephalic neural crest", - "xrefs" : [ "ZFA:0000935" ] + "val" : "textus connectivus collagenosus laxus", + "xrefs" : [ "FMA:19783", "FMA:TA" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "neural crest midbrain", - "xrefs" : [ "ZFA:0000935" ] + "val" : "textus connectivus laxus", + "xrefs" : [ "FMA:19783", "FMA:TA" ] } ], "xrefs" : [ { - "val" : "EFO:0003591" - }, { - "val" : "EHDAA2:0001101" - }, { - "val" : "EHDAA:360" + "val" : "FMA:19783" }, { - "val" : "TAO:0000935" + "val" : "NCIT:C33007" }, { - "val" : "VHOG:0000796" + "val" : "UMLS:C1253917" }, { - "val" : "ZFA:0000935" + "val" : "Wikipedia:Loose_connective_tissue" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27655,44 +29452,50 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003851", - "lbl" : "diencephalon neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011892", + "lbl" : "anterior uvea", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a diencephalon.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.", + "xrefs" : [ "MP:0005194" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "diencephalic neural crest", - "xrefs" : [ "ZFA:0000811" ] + "val" : "Haller tunica vascula", + "xrefs" : [ "MP:0005194" ] }, { "pred" : "hasExactSynonym", - "val" : "future diencephalon neural crest", - "xrefs" : [ "EHDAA2:0000603" ] + "val" : "anterior part of uveal tract" }, { "pred" : "hasExactSynonym", - "val" : "neural crest diencephalon", - "xrefs" : [ "ZFA:0000811" ] + "val" : "anterior uveal tract" }, { "pred" : "hasExactSynonym", - "val" : "neural crest of future diencephalon", - "xrefs" : [ "EMAPA:16518" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003573" + "val" : "anterior vascular layer of the eyeball" }, { - "val" : "EHDAA2:0000603" + "pred" : "hasExactSynonym", + "val" : "anterior vascular tunic of the eye" + }, { + "pred" : "hasExactSynonym", + "val" : "tunica vasculosa bulbosa", + "xrefs" : [ "MP:0005194" ] }, { - "val" : "EMAPA:16518" + "pred" : "hasExactSynonym", + "val" : "ventral uveal tract" }, { - "val" : "TAO:0000811" + "pred" : "hasRelatedSynonym", + "val" : "ciliary body and iris" }, { - "val" : "VHOG:0000798" + "pred" : "hasRelatedSynonym", + "val" : "vasculosa oculi", + "xrefs" : [ "MP:0005194" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37417" }, { - "val" : "ZFA:0000811" + "val" : "SCTID:280656002" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27700,72 +29503,66 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003852", - "lbl" : "rhombencephalon neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", + "lbl" : "coelom", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural crest hindbrain", - "xrefs" : [ "ZFA:0007063" ] + "pred" : "hasNarrowSynonym", + "val" : "enterocoelom", + "xrefs" : [ "NCBITaxon:33511" ] }, { - "pred" : "hasExactSynonym", - "val" : "rhombencephalic neural crest", - "xrefs" : [ "ZFA:0007063" ] + "pred" : "hasNarrowSynonym", + "val" : "haemocoelom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "schizocoelom" }, { "pred" : "hasRelatedSynonym", - "val" : "rhombomere neural crest", - "xrefs" : [ "EMAPA:35747" ] + "val" : "coelem" + }, { + "pred" : "hasRelatedSynonym", + "val" : "coelomic cavity", + "xrefs" : [ "EHDAA2:0004731" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0001628" - }, { - "val" : "EHDAA:362" - }, { - "val" : "EMAPA:35747" - }, { - "val" : "TAO:0007063" - }, { - "val" : "VHOG:0001210" + "val" : "EHDAA2:0004731" }, { - "val" : "ZFA:0007063" + "val" : "Wikipedia:Coelom" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003853", - "lbl" : "spinal cord neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", + "lbl" : "meso-epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.", + "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", "xrefs" : [ "OBOL:automatic" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neural crest spinal cord", - "xrefs" : [ "VHOG:0001006" ] + "val" : "mesoderm-derived epithelium" }, { - "pred" : "hasRelatedSynonym", - "val" : "spinal neural crest", - "xrefs" : [ "VHOG:0001006" ] + "pred" : "hasExactSynonym", + "val" : "mesoepithelium" } ], "xrefs" : [ { - "val" : "EHDAA:696" - }, { - "val" : "EMAPA:16163" - }, { - "val" : "EMAPA:16881" - }, { - "val" : "VHOG:0001006" + "val" : "FMA:86452" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27773,256 +29570,176 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "lbl" : "future coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012430", + "lbl" : "tunica fibrosa of eyeball", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.", + "xrefs" : [ "Wikipedia:Fibrous_tunic_of_eyeball" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "tunica fibrosa" + }, { "pred" : "hasExactSynonym", - "val" : "future coelomic cavity lumen" + "val" : "fibrous layer of eyeball", + "xrefs" : [ "FMA:58102" ] }, { "pred" : "hasRelatedSynonym", - "val" : "body cavity precursor" + "val" : "corneosclera", + "xrefs" : [ "Wikipedia:Fibrous_tunic_of_eyeball" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "fibrous tunic", + "xrefs" : [ "Wikipedia:Fibrous_tunic_of_eyeball" ] + } ], + "xrefs" : [ { + "val" : "FMA:58102" + }, { + "val" : "SCTID:361318005" + }, { + "val" : "Wikipedia:Fibrous_tunic_of_eyeball" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", - "lbl" : "intraembryonic coelom", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012467", + "lbl" : "enclosed anatomical space", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", - "xrefs" : [ "MGI:anna", "MP:0012187" ] + "val" : "An anatomical space with no opening to another space or to the exterior.", + "xrefs" : [ "AEO:0000222" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "somatic coelom", - "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] + "val" : "closed anatomical space" } ], "xrefs" : [ { - "val" : "EHDAA:251" - }, { - "val" : "EMAPA:16088" - }, { - "val" : "NCIT:C34195" - }, { - "val" : "UMLS:C1512940" - }, { - "val" : "VHOG:0000316" - }, { - "val" : "Wikipedia:Intraembryonic_coelom" + "val" : "AEO:0000222" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "lbl" : "stroma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", + "lbl" : "subdivision of tube", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Connective, non-functional supportive framework of a biological cell, tissue, or organ. 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"id" : "http://purl.obolibrary.org/obo/UBERON_0003914", - "lbl" : "epithelial tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", + "lbl" : "main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", - "xrefs" : [ "GO:0060562", "PMID:12526790" ] + "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial or endothelial tube" - } ], - "xrefs" : [ { - "val" : "AEO:0000114" - }, { - "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003931", - "lbl" : "diencephalic white matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", + "lbl" : "body proper", "type" : "CLASS", "meta" : { "definition" : { - "val" : "White matter that is part of a diencephalon [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The region of the organism associated with the visceral organs.", + "xrefs" : [ "AEO:0000103" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "diencephalic tract/commissure", - "xrefs" : [ "ZFA:0000338" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "diencephalic tracts and commissures", - "xrefs" : [ "TAO:0000338" ] - }, { - "pred" : "hasExactSynonym", - "val" : "predominantly white regional part of diencephalon", - "xrefs" : [ "BIRNLEX:1678" ] + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103" ] }, { - "pred" : "hasExactSynonym", - "val" : "white matter of diencephalon", - "xrefs" : [ "FMA:83931" ] + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1678" - }, { - "val" : "FMA:83931" + "val" : "AEO:0000103" }, { - "val" : "TAO:0000338" + "val" : "BTO:0001489" }, { - "val" : "ZFA:0000338" + "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0023148" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004022", - "lbl" : "germinal neuroepithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "lbl" : "mesenchyme derived from neural crest", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.", - "xrefs" : [ "MP:0004261", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "Mesenchyme that develops_from the neural crest[Automatically generated definition].", + "xrefs" : [ "OBOL:automatic", "https://github.com/obophenotype/uberon/issues/248" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "germinal neuroepithelial layer", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "mesenchyme from neural crest" }, { "pred" : "hasExactSynonym", - "val" : "germinal neuroepithelium", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "neural crest derived mesenchyme" }, { "pred" : "hasExactSynonym", - "val" : "original neural tube", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "neural crest mesenchyme" + } ], + "xrefs" : [ { + "val" : "EMAPA:32735" + }, { + "val" : "FMA:293883" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28030,78 +29747,56 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004060", - "lbl" : "neural tube ventricular layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", + "lbl" : "thoracic skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.", - "xrefs" : [ "MP:0009689", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", + "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ependymal layer", - "xrefs" : [ "NCBIBook:NBK10047" ] - }, { "pred" : "hasExactSynonym", - "val" : "neural tube ependymal layer", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "skeleton of thorax" }, { "pred" : "hasExactSynonym", - "val" : "neural tube ventricular germinal zone", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "thoracic part of axial skeleton" }, { "pred" : "hasExactSynonym", - "val" : "neural tube ventricular zone", - "xrefs" : [ "MP:0009689" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "neural tube ependymal zone", - "xrefs" : [ "MP:0009689" ] + "val" : "thoracic skeleton", + "xrefs" : [ "EHDAA2:0002013" ] } ], "xrefs" : [ { - "val" : "EMAPA:17152" - }, { - "val" : "EMAPA:35362" + "val" : "EHDAA2:0002013" }, { - "val" : "EMAPA_RETIRED:16783" + "val" : "FMA:77169" }, { - "val" : "MA:0003193" + "val" : "Wikipedia:Thoracic_skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004061", - "lbl" : "neural tube mantle layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", + "lbl" : "primordial vasculature", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.", - "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "A portion of tissue that will develop into vasculature.", + "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural tube intermediate zone", - "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "future brain marginal layer", - "xrefs" : [ "EMAPA:35360" ] - } ], "xrefs" : [ { - "val" : "EMAPA:17148" + "val" : "EFO:0003708" }, { - "val" : "EMAPA:35360" + "val" : "TAO:0005076" }, { - "val" : "neuronames:1367" + "val" : "ZFA:0005076" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28109,27 +29804,18 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004062", - "lbl" : "neural tube marginal layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015203", + "lbl" : "non-connected functional system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.", - "xrefs" : [ "MP:0009691", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "An anatomical group whose component structures share a common function.", + "xrefs" : [ "AEO:0000093", "AEO:JB", "FBC:DOS", "FBbt:00007278" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural tube marginal zone", - "xrefs" : [ "MP:0009691" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "brain marginal zone" - } ], "xrefs" : [ { - "val" : "EMAPA:17151" + "val" : "AEO:0000093" }, { - "val" : "neuronames:1368" + "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28137,122 +29823,88 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004088", - "lbl" : "orbital region", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", + "lbl" : "lateral structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present.", + "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "content of orbital part of eye", - "xrefs" : [ "FMA:260119" ] - }, { - "pred" : "hasExactSynonym", - "val" : "eye region", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "orbital part of face", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular and peri-ocular region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "orbital content", - "xrefs" : [ "FMA:260119" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "orbital part of eye", - "xrefs" : [ "FMA:72951" ] - } ], - "xrefs" : [ { - "val" : "FMA:260119" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004111", - "lbl" : "anatomical conduit", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", + "lbl" : "circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any tube, opening or passage that connects two distinct anatomical spaces.", + "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "foramen", - "xrefs" : [ "EHDAA2:0003080" ] + "pred" : "hasBroadSynonym", + "val" : "heart" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasNarrowSynonym", - "val" : "foramina", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "pred" : "hasExactSynonym", + "val" : "cardiac pump" }, { - "pred" : "hasRelatedSynonym", - "val" : "opening" + "pred" : "hasExactSynonym", + "val" : "heart or heart like organ" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "ostia" + "pred" : "hasNarrowSynonym", + "val" : "circulatory vessel" }, { "pred" : "hasRelatedSynonym", - "val" : "ostium" - } ], - "xrefs" : [ { - "val" : "AEO:0000080" - }, { - "val" : "EHDAA2:0003080" - }, { - "val" : "FMA:242873" - }, { - "val" : "SCTID:346902003" - }, { - "val" : "Wikipedia:Foramen" + "val" : "cardiac structure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", + "lbl" : "heart plus pericardium", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "heart/pericardium", + "xrefs" : [ "MA:0002449" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37597" }, { + "val" : "MA:0002449" + } ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004120", - "lbl" : "mesoderm-derived structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015808", + "lbl" : "eye epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure that develops (entirely or partially) from the mesoderm.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "An epithelium that is part of a camera-type eye.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesodermal derivative", - "xrefs" : [ "FBbt:00025998" ] + "xrefs" : [ { + "val" : "EMAPA:35957" + }, { + "val" : "MA:0003162" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28260,161 +29912,108 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004121", - "lbl" : "ectoderm-derived structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", + "lbl" : "future central nervous system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure that develops (entirely or partially) from the ectoderm.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "Primordium that develops into the central nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "ectodermal deriviative", - "xrefs" : [ "FBbt:00025990" ] + "val" : "future CNS" + }, { + "pred" : "hasExactSynonym", + "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000469" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004128", - "lbl" : "optic vesicle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", + "lbl" : "future nervous system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].", - "xrefs" : [ "GO:0003404", "Wikipedia:Optic_vesicles" ] + "val" : "Primordium that develops into the nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 \"Developmental Biology\"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "evagination" - }, { - "pred" : "hasRelatedSynonym", - "val" : "eye vesicle", - "xrefs" : [ "XAO:0000228" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular vesicle", - "xrefs" : [ "VHOG:0000165" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "optic vesicles", - "xrefs" : [ "ZFA:0000050" ] + "pred" : "hasExactSynonym", + "val" : "presumptive nervous system", + "xrefs" : [ "AAO:0000477" ] } ], "xrefs" : [ { - "val" : "AAO:0011039" - }, { - "val" : "EHDAA2:0001320" - }, { - "val" : "EMAPA:16540" - }, { - "val" : "FMA:293357" - }, { - "val" : "NCIT:C34236" - }, { - "val" : "SCTID:362864008" - }, { - "val" : "TAO:0000050" - }, { - "val" : "UMLS:C0231106" - }, { - "val" : "VHOG:0000165" - }, { - "val" : "Wikipedia:Optic_vesicles" - }, { - "val" : "XAO:0000228" - }, { - "val" : "ZFA:0000050" + "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000477" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", - "lbl" : "cardiogenic plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016887", + "lbl" : "entire extraembryonic component", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The first recognizable structure derived from the heart field.", - "xrefs" : [ "GO:0003142" ] + "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", + "xrefs" : [ "AEO:0000195", "AEO:JB" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "myocardial plate", - "xrefs" : [ "EHDAA2:0000215" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac crescent", - "xrefs" : [ "EMAPA:16106" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiogenic crescent", - "xrefs" : [ "GO:0003142" ] + "val" : "extra-embryonic component" }, { - "pred" : "hasRelatedSynonym", - "val" : "heart rudiment" + "pred" : "hasExactSynonym", + "val" : "extraembryonic component", + "xrefs" : [ "AEO:0000195" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0000215" + "val" : "AEO:0000195" }, { - "val" : "EMAPA:16106" + "val" : "EHDAA2:0000003" }, { - "val" : "VHOG:0000975" + "val" : "EMAPA:16042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", - "lbl" : "primary heart field", + "id" : "http://purl.obolibrary.org/obo/UBERON_0019207", + "lbl" : "chorioretinal region", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", - "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] + "val" : "The part of the eye that consists of both the retina and the optic choroid.", + "xrefs" : [ "UBERON:drseb", "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "first heart field", - "xrefs" : [ "XAO:0004185" ] + "val" : "chorioretina" }, { "pred" : "hasExactSynonym", - "val" : "primary heart field", - "xrefs" : [ "PMID:17276708", "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "FHF", - "xrefs" : [ "XAO:0004185" ] + "val" : "choroid and retina" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "PHF", - "xrefs" : [ "XAO:0004185" ] + "pred" : "hasExactSynonym", + "val" : "retinachoroid" }, { - "pred" : "hasRelatedSynonym", - "val" : "heart field", - "xrefs" : [ "XAO:0004185" ] + "pred" : "hasExactSynonym", + "val" : "retinachoroidal region" } ], "xrefs" : [ { - "val" : "XAO:0004185" + "val" : "SCTID:110701000" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28422,42 +30021,37 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", - "lbl" : "heart tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0019261", + "lbl" : "white matter of forebrain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelial tube that will give rise to the mature heart.", - "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] + "val" : "A white matter that is part of the forebrain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic heart tube", - "xrefs" : [ "GO:0003143" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial heart tube", - "xrefs" : [ "MP:0012700" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial tube", - "xrefs" : [ "XAO:0000337" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { - "val" : "AAO:0010411" - }, { - "val" : "EFO:0003526" - }, { - "val" : "EMAPA:32685" - }, { - "val" : "NCIT:C34161" + "val" : "DHBA:10557" }, { - "val" : "TAO:0000360" + "val" : "FMA:268634" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "XAO:0000337" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0019304", + "lbl" : "sensory organ epithelium", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EMAPA:35952" }, { - "val" : "ZFA:0000360" + "val" : "MA:0003174" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28465,26 +30059,17 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", - "lbl" : "cardiac chamber", + "id" : "http://purl.obolibrary.org/obo/UBERON_0022288", + "lbl" : "surface of eyeball", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", - "xrefs" : [ "GO:0003205" ] - }, - "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chamber of heart" - }, { - "pred" : "hasExactSynonym", - "val" : "heart chamber" + "pred" : "hasRelatedSynonym", + "val" : "surface of region of wall of eyeball", + "xrefs" : [ "FMA:58315" ] } ], "xrefs" : [ { - "val" : "FMA:7095" - }, { - "val" : "SCTID:276456008" + "val" : "FMA:58315" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28492,108 +30077,82 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004277", - "lbl" : "eye muscle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0022303", + "lbl" : "nervous system cell part layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A muscle that is part of the eye region.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].", + "xrefs" : [ "NLX:149357" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "AAO:0000156" - }, { - "val" : "EMAPA:35335" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "lamina", + "xrefs" : [ "CUMBO:CUMBO" ] }, { - "val" : "MA:0000271" + "pred" : "hasBroadSynonym", + "val" : "layer", + "xrefs" : [ "CUMBO:CUMBO" ] + } ], + "xrefs" : [ { + "val" : "NLX:149357" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034705", + "lbl" : "developing neuroepithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "An embryonic or larval epithelium that is committed to form part of the nervous system.", + "xrefs" : [ "AEO:0001008", "AEO:JB" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "neurepithelium", + "xrefs" : [ "BTO:0000314" ] + }, { "pred" : "hasExactSynonym", - "val" : "set of all bones" + "val" : "embryonic neuroepithelium", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "set of bones of body" + "val" : "neuroepithelium", + "xrefs" : [ "AEO:0001008" ] } ], "xrefs" : [ { - "val" : "AEO:0000168" - }, { - "val" : "EHDAA2:0001843" - }, { - "val" : "EHDAA:5047" - }, { - "val" : "EMAPA:17213" - }, { - "val" : "FMA:23875" - }, { - "val" : "GAID:177" - }, { - "val" : "MA:0003006" - }, { - "val" : "MAT:0000032" - }, { - "val" : "MESH:D012863" - }, { - "val" : "MIAA:0000032" - }, { - "val" : "SCTID:361378004" - }, { - "val" : "VSAO:0000026" + "val" : "AEO:0001008" }, { - "val" : "Wikipedia:Skeleton" + "val" : "BTO:0000314" }, { - "val" : "XAO:0004053" + "val" : "EHDAA2_RETIRED:0004654" }, { - "val" : "galen:Skeleton" + "val" : "FMA:64807" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004291", - "lbl" : "heart rudiment", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034706", + "lbl" : "proliferating neuroepithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.", - "xrefs" : [ "GO:0003313" ] + "val" : "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.", + "xrefs" : [ "AEO:0001009" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart cone", - "xrefs" : [ "GO:0003313" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rudimentary heart", - "xrefs" : [ "ZFA:0000115" ] - } ], "xrefs" : [ { - "val" : "TAO:0000115" - }, { - "val" : "ZFA:0000115" + "val" : "AEO:0001009" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28601,23 +30160,16 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004348", - "lbl" : "optic eminence", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034707", + "lbl" : "differentiating neuroepithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The embryonic structure that gives rise to the corneal ectoderm.", - "xrefs" : [ "MP:0006305" ] + "val" : "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.", + "xrefs" : [ "AEO:0001010" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "xrefs" : [ { - "val" : "EHDAA:938" - }, { - "val" : "EMAPA:16322" - }, { - "val" : "RETIRED_EHDAA2:0001308" - }, { - "val" : "VHOG:0001296" + "val" : "AEO:0001010" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28625,4386 +30177,3545 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004367", - "lbl" : "Descemet's membrane", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034713", + "lbl" : "cranial neuron projection bundle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].", - "xrefs" : [ "MP:0004285", "https://github.com/obophenotype/uberon/issues/15" ] + "val" : "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.", + "xrefs" : [ "ISBN:0471888893", "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Descemet membrane" - }, { - "pred" : "hasExactSynonym", - "val" : "Descemet's posterior elastic lamina", - "xrefs" : [ "FMA:58309" ] - }, { - "pred" : "hasExactSynonym", - "val" : "lamina limitans posterior", - "xrefs" : [ "FMA:58309" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "lamina limitans posterior corneae", - "xrefs" : [ "FMA:58309", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior limiting lamina", - "xrefs" : [ "MA:0001246" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior limiting lamina of cornea", - "xrefs" : [ "FMA:58309" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior limiting membrane", - "xrefs" : [ "ZFA:0001686" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:18804" - }, { - "val" : "FMA:58309" - }, { - "val" : "GAID:894" - }, { - "val" : "MA:0001246" - }, { - "val" : "MESH:D003886" - }, { - "val" : "NCIT:C32454" - }, { - "val" : "SCTID:281076002" - }, { - "val" : "TAO:0002157" + "pred" : "hasRelatedSynonym", + "val" : "cranial nerve fiber bundle", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "UMLS:C0011665" + "pred" : "hasRelatedSynonym", + "val" : "cranial nerve fiber tract", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "Wikipedia:Descemet%27s_membrane" + "pred" : "hasRelatedSynonym", + "val" : "cranial nerve or tract", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "ZFA:0001686" + "pred" : "hasRelatedSynonym", + "val" : "neuron projection bundle from brain", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/15" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004370", - "lbl" : "anterior limiting lamina of cornea", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", + "lbl" : "multi organ part structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; 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A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "val" : "EHDAA2:0003235" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "EMAPA:36040" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "NCIT:C34131" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "UMLS:C1516779" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "val" : "Wikipedia:Conceptus" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004732", - "lbl" : "segmental subdivision of nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.", - "xrefs" : [ "FBbt:00005140", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neuromere", - "xrefs" : [ "FBbt:00005140" ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004733", - "lbl" : "segmental subdivision of hindbrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ subunit that is part of a hindbrain [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hindbrain segment", - "xrefs" : [ "FMA:61998" ] - }, { - "pred" : "hasExactSynonym", - "val" : "segment of hindbrain", - "xrefs" : [ "FMA:61998" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "FMA:61998" + "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", - "lbl" : "gastrula", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the gastrula stage.", - "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gastrula embryo", - "xrefs" : [ "BILA:0000060" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocystis trilaminaris", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastocyst", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar germ", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } ], + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BILA:0000060" - }, { - "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" - }, { - "val" : "FMA:293108" - }, { - "val" : "GAID:1302" - }, { - "val" : "MESH:D005775" - }, { - "val" : "MIAA:0000179" - }, { - "val" : "NCIT:C34057" - }, { - "val" : "NCIT:C34058" - }, { - "val" : "UMLS:C0017199" - }, { - "val" : "UMLS:C1284022" - }, { - "val" : "Wikipedia:Gastrula" - }, { - "val" : "Wikipedia:Trilaminar_blastocyst" + "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", - "lbl" : "skeletal element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" - }, { - "val" : "galen:SkeletalStructure" + "val" : "GOREL:0002003" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" - }, { - "val" : "MA:0003007" - }, { - "val" : "SCTID:361827000" - }, { - "val" : "VSAO:0000181" + "val" : "GOREL:0002004" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", - "lbl" : "cardiovascular system endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that is part of the cardiovascular system.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "endothelia", - "xrefs" : [ "ZFA:0001639" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "vascular endothelia", - "xrefs" : [ "XAO:0000356" ] - } ], "xrefs" : [ { - "val" : "BTO:0001853" - }, { - "val" : "EMAPA:35201" - }, { - "val" : "GAID:519" - }, { - "val" : "MA:0000717" - }, { - "val" : "MESH:D004730" - }, { - "val" : "NCIT:C13053" - }, { - "val" : "TAO:0002171" - }, { - "val" : "UMLS:C0014261" - }, { - "val" : "VHOG:0001217" - }, { - "val" : "XAO:0000356" - }, { - "val" : "ZFA:0001639" + "val" : "RO:0000053" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'endothelium'" + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004872", - "lbl" : "splanchnic layer of lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" ] + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "visceral mesoderm", - "xrefs" : [ "BILA:0000044", "http://www.drugs.com/dict/visceral-mesoderm.html", "http://www.stedmans.com/" ] - }, { - "pred" : "hasExactSynonym", - "val" : "inner layer of lateral plate mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - } ], "xrefs" : [ { - "val" : "AAO:0011102" - }, { - "val" : "BILA:0000044" - }, { - "val" : "FMA:295568" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" - }, { - "val" : "XAO:0000276" + "val" : "RO:0000056" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], "xrefs" : [ { - "val" : "AAO:0000478" - }, { - "val" : "EFO:0003426" - }, { - "val" : "TAO:0000091" - }, { - "val" : "ZFA:0000091" + "val" : "RO:0000057" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004905", - "lbl" : "articulation", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A proximal-distal subdivision of the digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system subdivision", - "xrefs" : [ "FMA:71131" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut section", - "xrefs" : [ "FBbt:00100315" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "segment of intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "subdivision of alimentary system", - "xrefs" : [ "FMA:71131" ] - } ], - "xrefs" : [ { - "val" : "FBbt:00100315" - }, { - "val" : "FMA:71131" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "lbl" : "organ component layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A part of a wall of an organ that forms a layer.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FMA:82485" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005061", - "lbl" : "neural groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.", - "xrefs" : [ "GO:0001842", "Wikipedia:Neural_groove", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "xrefs" : [ { - "val" : "AAO:0011071" - }, { - "val" : "EMAPA:35594" - }, { - "val" : "FMA:295624" - }, { - "val" : "NCIT:C34224" - }, { - "val" : "SCTID:361463007" - }, { - "val" : "UMLS:C0814992" - }, { - "val" : "Wikipedia:Neural_groove" - }, { - "val" : "XAO:0000248" - }, { - "val" : "neuronames:1363" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "lbl" : "neural fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "One of the two elevated edges of the neural groove[GO,MP].", - "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "medullary fold", - "xrefs" : [ "MP:0011256" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001249" - }, { - "val" : "FMA:295618" - }, { - "val" : "NCIT:C34223" - }, { - "val" : "SCTID:361461009" - }, { - "val" : "UMLS:C0814993" - }, { - "val" : "Wikipedia:Neural_fold" - }, { - "val" : "XAO:0004087" - }, { - "val" : "neuronames:1364" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005068", - "lbl" : "neural rod", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].", - "xrefs" : [ "GO:0014024", "ZFA:0000133" ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural tube rod", - "xrefs" : [ "GO:0014027" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003498" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "val" : "TAO:0000133" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "ZFA:0000133" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005085", - "lbl" : "ectodermal placode", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO].", - "xrefs" : [ "GO:0060788" ] + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "epithelial placode", - "xrefs" : [ "AEO:0000112" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000218" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "lbl" : "muscle structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", - "xrefs" : [ "GO:0061061" ] + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "musculus", - "xrefs" : [ "FMA:30316" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle element" - } ], - "xrefs" : [ { - "val" : "FMA:30316" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", - "lbl" : "epithelial fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelial sheet bent on a linear axis.", - "xrefs" : [ "GO:0060571" ] + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005162", - "lbl" : "multi cell part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.", - "xrefs" : [ "CARO:0001000" ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multi-cell-component structure", - "xrefs" : [ "CARO:0001000" ] - }, { - "pred" : "hasExactSynonym", - "val" : "multi-cell-part structure", - "xrefs" : [ "CARO:0001000" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cell part cluster", - "xrefs" : [ "FMA:83115" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011000" - }, { - "val" : "CARO:0001000" - }, { - "val" : "FBbt:00007060" - }, { - "val" : "FMA:83115" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005174", - "lbl" : "dorsal region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "back organ", - "xrefs" : [ "MA:0001901" ] - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal region organ" - } ], + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "xrefs" : [ { - "val" : "EMAPA:37274" - }, { - "val" : "MA:0001901" + "val" : "RO:0002087" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", - "lbl" : "trunk region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An organ or element that part of the trunk region. 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Examples: lung, heart, longus colli.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracic cavity organ", - "xrefs" : [ "MA:0000557" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37273" - }, { - "val" : "MA:0000557" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", - "lbl" : "thoracic segment organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that part of the thoracic segment region. 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There are no endoneurium and schwann cells in the central nervous system.", - "xrefs" : [ "Wikipedia:Nervous_system_fiber" ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "comments" : [ "This is the transitive form of the develops from relation" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nerve fibre", - "xrefs" : [ "FMA:5914" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "neurofibra", - "xrefs" : [ "FMA:5914", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neurofibrum", - "xrefs" : [ "FMA:5914" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "nerve fibers", - "xrefs" : [ "BAMS:nfi" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "neurofibra", - "xrefs" : [ "Wikipedia:Nerve_fiber" ] - } ], - "xrefs" : [ { - "val" : "BAMS:nfi" - }, { - "val" : "FMA:5914" - }, { - "val" : "MESH:D009412" - }, { - "val" : "SCTID:88545005" - }, { - "val" : "Wikipedia:Nervous_system_fiber" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "has developmental precursor" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006135", - "lbl" : "myelinated nerve fiber", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH).", - "xrefs" : [ "ncithesaurus:Myelinated_Nerve_Fiber" ] + "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "FMA:5915" - }, { - "val" : "GAID:745" - }, { - "val" : "MESH:D009413" - }, { - "val" : "NCIT:C12627" - }, { - "val" : "SCTID:362296008" - }, { - "val" : "UMLS:C0027750" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding link to UBERON:0002316 ! white matter of neuraxis" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117569" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006222", - "lbl" : "future diencephalon", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The foremost region of the future forebrain that develops into the diencephalon.", - "xrefs" : [ "UBERON:cjm", "Wikipedia:Diencephalon" ] + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive diencephalon", - "xrefs" : [ "TAO:0000574" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EFO:0003442" - }, { - "val" : "EHDAA2:0000600" - }, { - "val" : "EHDAA:844" - }, { - "val" : "EMAPA:16514" - }, { - "val" : "RETIRED_EHDAA2:0000386" - }, { - "val" : "TAO:0000574" - }, { - "val" : "ZFA:0000574" + "val" : "RO:0002211" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006238", - "lbl" : "future brain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The embryonic precursor of the brain.", - "xrefs" : [ "NLX:94995" ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "brain rudiment", - "xrefs" : [ "TAO:0000146" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive brain", - "xrefs" : [ "ZFA:0000146" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "encephalon", - "xrefs" : [ "NLX:94995" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic brain", - "xrefs" : [ "BTO:0004726" ] - } ], - "xrefs" : [ { - "val" : "BAMS:Enc" - }, { - "val" : "BTO:0004726" - }, { - "val" : "EFO:0003431" - }, { - "val" : "EHDAA:300" - }, { - "val" : "EHDAA:830" - }, { - "val" : "EMAPA:16089" - }, { - "val" : "FMA:312967" - }, { - "val" : "RETIRED_EHDAA2:0000591" - }, { - "val" : "TAO:0000146" - }, { - "val" : "ZFA:0000146" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006240", - "lbl" : "future forebrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A presumptive structure that has the potential to develop into a forebrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future prosencephalon" - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive forebrain", - "xrefs" : [ "ZFA:0000062" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive prosencephalon", - "xrefs" : [ "TAO:0000062" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "prosencephalon", - "xrefs" : [ "EHDAA2:0000661" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BAMS:Pros" - }, { - "val" : "EFO:0003423" - }, { - "val" : "EHDAA2:0000661" - }, { - "val" : "EHDAA:2643" - }, { - "val" : "EMAPA:16640" - }, { - "val" : "TAO:0000062" - }, { - "val" : "Wikipedia:Prosencephalon" - }, { - "val" : "ZFA:0000062" + "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006241", - "lbl" : "future spinal cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord", - "xrefs" : [ "ZFA:0000417" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord neural keel", - "xrefs" : [ "TAO:0000417" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord neural plate", - "xrefs" : [ "TAO:0000417" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord neural rod", - "xrefs" : [ "TAO:0000417" ] - } ], + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "EFO:0003438" - }, { - "val" : "EHDAA2:0000674" - }, { - "val" : "EHDAA:898" - }, { - "val" : "EMAPA:16092" - }, { - "val" : "EMAPA:16755" - }, { - "val" : "TAO:0000417" - }, { - "val" : "ZFA:0000417" + "val" : "RO:0002215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", - "lbl" : "notochordal plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", - "xrefs" : [ "VHOG:0001212" ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "xrefs" : [ { - "val" : "EHDAA2:0001278" - }, { - "val" : "EHDAA:264" - }, { - "val" : "EMAPA:16101" - }, { - "val" : "NCIT:C34231" + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "UMLS:C1518429" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" }, { - "val" : "VHOG:0001212" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check ordering; awaiting confirmation from JB" + "val" : "This relation acts as a join point with BSPO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "lbl" : "notochordal process", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", - "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] + "val" : "inverse of surrounded by" }, - "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive notochord" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "EHDAA2:0001279" - }, { - "val" : "EHDAA:224" - }, { - "val" : "EMAPA:16102" - }, { - "val" : "FMA:293135" - }, { - "val" : "NCIT:C34232" - }, { - "val" : "UMLS:C1518430" - }, { - "val" : "VHOG:0001213" + "val" : "RO:0002224" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006311", - "lbl" : "chamber of eyeball", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A segment of the eyeball that is filled with refractive media.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of ends with" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "eye chamber", - "xrefs" : [ "MA:0002459" ] - }, { - "pred" : "hasExactSynonym", - "val" : "eyeball chamber", - "xrefs" : [ "FMA:58071" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "chamber of eye", - "xrefs" : [ "BTO:0002085" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BTO:0002085" - }, { - "val" : "EMAPA:37529" - }, { - "val" : "FMA:58071" - }, { - "val" : "MA:0002459" - }, { - "val" : "NCIT:C32301" - }, { - "val" : "SCTID:280540004" - }, { - "val" : "UMLS:C0459556" + "val" : "RO:0002230" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006312", - "lbl" : "ocular refractive media", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - 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Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007619", - "lbl" : "limiting membrane of retina", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "retina lamina", - "xrefs" : [ "MA:0001318", "https://github.com/obophenotype/uberon/issues/52" ] - } ], - "xrefs" : [ { - "val" : "MA:0001318" + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" }, { - "val" : "SCTID:280667001" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007625", - "lbl" : "pigment epithelium of eye", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.", - "xrefs" : [ "MP:0005200" ] + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "eye pigment epithelium", - "xrefs" : [ "MESH:A09.371.670" ] - } ], "xrefs" : [ { - "val" : "GAID:907" - }, { - "val" : "MESH:D010857" + "val" : "RO:0002404" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007651", - "lbl" : "anatomical junction", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical structure that connects two structures.", - "xrefs" : [ "http://code.google.com/p/caro2/issues/detail?id=15" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "junction" - }, { - "pred" : "hasExactSynonym", - "val" : "anatomical junction" - } ], - "xrefs" : [ { - "val" : "FMA:5898" - }, { - "val" : "SCTID:91833003" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007688", - "lbl" : "anlage", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.", - "xrefs" : [ "FBbt:00005426", "http://flybase.org/reports/FBrf0178740.html" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - 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"val" : "An axon tract that is part of a brain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "brain tract", - "xrefs" : [ "FMA:83848" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "landmark tracts", - "xrefs" : [ "DMBA:tracts" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "FMA:83848" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - 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"val" : "consider merging with vasculature" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007811", - "lbl" : "craniocervical region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cephalic area", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cephalic part of animal", - "xrefs" : [ "Wikipedia:Head" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cephalic region", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "head and neck", - "xrefs" : [ "FMA:280881" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "head or neck" - } ], - "xrefs" : [ { - "val" : "CALOHA:TS-2356" - }, { - "val" : "EV:0100009" - }, { - "val" : "FMA:280881" - }, { - "val" : "MA:0000006" - }, { - "val" : "NCIT:C12418" - }, { - "val" : "SCTID:361355005" - }, { - "val" : "UMLS:C0460004" - }, { - "val" : "WikipediaCategory:Head_and_neck" - }, { - "val" : "galen:HeadAndNeck" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", - "lbl" : "entire embryonic mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Sum total of mesenchyme in the embryo.", - "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, - "xrefs" : [ { - "val" : "EHDAA2:0001113" - }, { - "val" : "EHDAA:177" - }, { - "val" : "EMAPA:16097" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "OWL does not allow defining object properties via a Union" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", - "lbl" : "subdivision of trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "region of trunk", - "xrefs" : [ "FMA:25054" ] - }, { - "pred" : "hasExactSynonym", - "val" : "trunk subdivision", - "xrefs" : [ "FMA:25054" ] - } ], - "xrefs" : [ { - "val" : "FMA:25054" - }, { - "val" : "SCTID:22943007" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009581", - "lbl" : "midbrain mantle layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mantle layer lateral wall midbrain", - "xrefs" : [ "VHOG:0000910" ] - }, { - "pred" : "hasExactSynonym", - "val" : "midbrain lateral wall mantle layer" - }, { - "pred" : "hasRelatedSynonym", - "val" : "mantle layer lateral wall mesencephalon", - "xrefs" : [ "VHOG:0000910" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001172" - }, { - "val" : "EMAPA:16977" - }, { - "val" : "VHOG:0000910" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009615", - "lbl" : "midbrain hindbrain boundary neural plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "MHB neural plate", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "midbrain-hindbrain boundary neural plate", - "xrefs" : [ "ZFA:0007044" ] - } ], - "xrefs" : [ { - "val" : "TAO:0007044" - }, { - "val" : "ZFA:0007044" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - developmental relationships for lines" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009616", - "lbl" : "presumptive midbrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A presumptive structure that has the potential to develop into a midbrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive mesencephalon", - "xrefs" : [ "ZFA:0000148" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "early midbrain", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "future midbrain", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mesencephalon", - "xrefs" : [ "EHDAA2:0000615" ] - } ], - "xrefs" : [ { - "val" : "BAMS:MES" - }, { - "val" : "EFO:0003432" - }, { - "val" : "EHDAA2:0000615" - }, { - "val" : "EMAPA:16140" - }, { - "val" : "TAO:0000148" - }, { - "val" : "Wikipedia:Mesencephalon" - }, { - "val" : "ZFA:0000148" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - unify naming conventions" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "lbl" : "trunk paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "trunk and cervical paraxial mesenchyme", - "xrefs" : [ "EHDAA2:0002094" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trunk paraxial mesenchyme", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002094" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "exists during" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009881", - "lbl" : "anterior lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - 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"synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "face mesenchyme" - }, { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of face" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:35337" - }, { - "val" : "FMA:302884" + "val" : "RO:0002565" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_movement_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009920", - "lbl" : "optic neural crest", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "EHDAA2:0001315" - 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"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multicellular structure", - "xrefs" : [ "FBbt:00100313" ] - } ], - "xrefs" : [ { - "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0010096", - 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Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0003000" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "produces" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0010371", - "lbl" : "ecto-epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelium composed of cells that develops from the ectoderm[FMA,modified].", - 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In most vertebrates this is the rib cage and sternum.", - "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "skeleton of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic part of axial skeleton" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic skeleton", - "xrefs" : [ "EHDAA2:0002013" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002013" - }, { - "val" : "FMA:77169" - }, { - "val" : "Wikipedia:Thoracic_skeleton" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", - "lbl" : "primordial vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", + "lbl" : "protects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A portion of tissue that will develop into vasculature.", - "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] - }, - "xrefs" : [ { - "val" : "EFO:0003708" - }, { - "val" : "TAO:0005076" - }, { - "val" : "ZFA:0005076" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015203", - "lbl" : "non-connected functional system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", + "lbl" : "proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical group whose component structures share a common function.", - "xrefs" : [ "AEO:0000093", "AEO:JB", "FBC:DOS", "FBbt:00007278" ] + "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "xrefs" : [ { - "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "lbl" : "lateral structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", + "lbl" : "sexually_homologous_to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", - "lbl" : "circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", + "lbl" : "site_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "heart" - }, { - "pred" : "hasExactSynonym", - "val" : "cardiac pump" - }, { - "pred" : "hasExactSynonym", - "val" : "heart or heart like organ" - }, { - "pred" : "hasNarrowSynonym", - "val" : "circulatory vessel" - }, { "pred" : "hasRelatedSynonym", - "val" : "cardiac structure" + "val" : "capable_of_has_part" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -33240,599 +33866,496 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", - "lbl" : "heart plus pericardium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", + "lbl" : "subdivision of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart/pericardium", - "xrefs" : [ "MA:0002449" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37597" - }, { - "val" : "MA:0002449" - } ], + "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015808", - "lbl" : "eye epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An epithelium that is part of a camera-type eye.", - "xrefs" : [ "OBOL:automatic" ] - }, - "xrefs" : [ { - "val" : "EMAPA:35957" - }, { - "val" : "MA:0003162" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - 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"type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "The part of the eye that consists of both the retina and the optic choroid.", - "xrefs" : [ "UBERON:drseb", "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chorioretina" - }, { - "pred" : "hasExactSynonym", - "val" : "choroid and retina" - }, { - "pred" : "hasExactSynonym", - "val" : "retinachoroid" - }, { - "pred" : "hasExactSynonym", - "val" : "retinachoroidal region" - } ], - "xrefs" : [ { - "val" : "SCTID:110701000" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0019261", - "lbl" : "white matter of forebrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A white matter that is part of the forebrain.", - "xrefs" : [ "OBOL:automatic" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "xrefs" : [ { - "val" : "DHBA:10557" - }, { - "val" : "FMA:268634" - } ], + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0019304", - "lbl" : "sensory organ epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", "meta" : { - "xrefs" : [ { - "val" : "EMAPA:35952" - }, { - "val" : "MA:0003174" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0022288", - "lbl" : "surface of eyeball", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "surface of region of wall of eyeball", - "xrefs" : [ "FMA:58315" ] - } ], - "xrefs" : [ { - "val" : "FMA:58315" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0022303", - "lbl" : "nervous system cell part layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].", - "xrefs" : [ "NLX:149357" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lamina", - "xrefs" : [ "CUMBO:CUMBO" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "layer", - "xrefs" : [ "CUMBO:CUMBO" ] - } ], - "xrefs" : [ { - "val" : "NLX:149357" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. 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At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034705", - "lbl" : "developing neuroepithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An embryonic or larval epithelium that is committed to form part of the nervous system.", - "xrefs" : [ "AEO:0001008", "AEO:JB" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "neurepithelium", - "xrefs" : [ "BTO:0000314" ] - }, { - "pred" : "hasExactSynonym", - "val" : "embryonic neuroepithelium", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neuroepithelium", - "xrefs" : [ "AEO:0001008" ] - } ], - "xrefs" : [ { - "val" : "AEO:0001008" - }, { - "val" : "BTO:0000314" - }, { - "val" : "EHDAA2_RETIRED:0004654" - }, { - "val" : "FMA:64807" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034706", - "lbl" : "proliferating neuroepithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.", - "xrefs" : [ "AEO:0001009" ] + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, - "xrefs" : [ { - "val" : "AEO:0001009" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034707", - "lbl" : "differentiating neuroepithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.", - "xrefs" : [ "AEO:0001010" ] + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, - "xrefs" : [ { - "val" : "AEO:0001010" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034713", - "lbl" : "cranial neuron projection bundle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.", - "xrefs" : [ "ISBN:0471888893", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cranial nerve fiber bundle", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cranial nerve fiber tract", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cranial nerve or tract", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neuron projection bundle from brain", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "xrefs" : [ { - "val" : "CARO:0020001" + "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" + "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035639", - "lbl" : "ocular adnexa", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.", - "xrefs" : [ "HPO:pr", "UBERON:cjm", "http://medical-dictionary.thefreedictionary.com/ocular+adnexa", "https://github.com/obophenotype/uberon/issues/1132" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "adnexa oculi", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory parts of orbital region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory visual structures", - "xrefs" : [ "FMA:76554", "Wikipedia:Accessory_visual_structures" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory visual structures set", - "xrefs" : [ "FMA:76554" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "adnexal parts of orbital region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "appendage of eye", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "appendages of the eye", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "eye adnexa" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of accessory visual structures", - "xrefs" : [ "FMA:76554" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "structurae oculi accessoriae", - "xrefs" : [ "Wikipedia:Accessory_visual_structures" ] - } ], - "xrefs" : [ { - "val" : "FMA:76554" - }, { - "val" : "NCIT:C32574" - }, { - "val" : "SCTID:120612006" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" }, { - "val" : "UMLS:C0229243" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" }, { - "val" : "Wikipedia:Accessory_visual_structures" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "A synonym type for describing abbreviations or initalisms" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], - "xrefs" : [ { - "val" : "FMA:293105" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036146", - "lbl" : "cardiopharyngeal field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.", - "xrefs" : [ "http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1", "https://orcid.org/0000-0003-3308-6245" ] + "val" : "A synonym type for describing pluralization synonyms" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036215", - "lbl" : "anatomical surface region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity that forms the outermost boundary of an anatomical structure.", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/1324" ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "AAO:0010270" - }, { - "val" : "ZFA:0005594" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", - "lbl" : "visceral muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, - "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral muscle" - } ], + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:17:46Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { @@ -33844,6 +34367,7 @@ "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } @@ -33851,49 +34375,15 @@ "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { @@ -33901,291 +34391,391 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", "lbl" : "latin term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", "lbl" : "plural term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "type" : "PROPERTY", - "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." - }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "type" : "PROPERTY", - "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -34201,11 +34791,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -34222,6 +34814,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -34237,11 +34830,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -34257,23 +34852,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -34283,6 +34907,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -34506,16 +35142,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000483" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000076", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "is_a", @@ -34596,8 +35222,8 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000213" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000117", "pred" : "is_a", @@ -34646,10 +35272,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000132", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000115" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000132", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000710" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000132", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36672,10 +37294,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044249" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009059", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_1901576" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -37844,10 +38462,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0070925", "pred" : "http://purl.obolibrary.org/obo/RO_0002588", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0071704", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0071826", "pred" : "is_a", @@ -38164,14 +38778,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140352", "pred" : "http://purl.obolibrary.org/obo/RO_0002339", "obj" : "http://purl.obolibrary.org/obo/GO_0005576" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1903047", "pred" : "is_a", @@ -38568,6 +39174,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070060", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002198" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -38692,6 +39310,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000036194", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "is_a", @@ -46315,6 +46937,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000005", @@ -46405,10 +47031,10 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000071", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000076" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0004638" + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", @@ -49012,6 +49638,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/src/ontology/subsets/eye_upper_slim.obo b/src/ontology/subsets/eye_upper_slim.obo index b4002a747..afc802901 100644 --- a/src/ontology/subsets/eye_upper_slim.obo +++ b/src/ontology/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -131,7 +136,7 @@ name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell @@ -142,21 +147,21 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] id: CL:0000008 name: migratory cranial neural crest cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] -xref: ZFA:0007091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000030 name: glioblast subset: cellxgene_subset -xref: ZFA:0009010 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -168,7 +173,7 @@ subset: cellxgene_subset synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 -xref: ZFA:0009011 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata @@ -184,7 +189,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -209,7 +214,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -257,7 +262,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -271,7 +276,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -294,7 +299,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -313,7 +318,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -331,7 +336,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -351,10 +356,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -370,7 +375,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -386,13 +391,13 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -401,12 +406,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -417,7 +420,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -426,7 +429,7 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] @@ -437,7 +440,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 -xref: ZFA:0009040 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell @@ -451,7 +454,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -471,10 +474,10 @@ def: "Most generally any neuron which is not motor or sensory. Interneurons may subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0003811 -xref: FBbt:00005125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67313 xref: WBbt:0005113 -xref: ZFA:0009051 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009051 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -484,11 +487,11 @@ name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] subset: human_reference_atlas xref: BTO:0001037 -xref: FBbt:00005124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 xref: MESH:D011984 xref: WBbt:0005759 -xref: ZFA:0009053 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009053 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000526 ! afferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception @@ -502,7 +505,7 @@ def: "A type of interneuron that has two neurites, usually an axon and a dendrit subset: BDS_subset subset: cellxgene_subset xref: FMA:67282 -xref: ZFA:0009055 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070006 ! cortical bipolar morphology @@ -519,15 +522,15 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) -xref: ZFA:0009067 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009067 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) @@ -553,9 +556,9 @@ synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: CALOHA:TS-0415 -xref: FBbt:00005144 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 -xref: ZFA:0009073 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 @@ -569,7 +572,7 @@ synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 xref: CALOHA:TS-2027 xref: FMA:54538 -xref: ZFA:0009074 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) @@ -584,7 +587,7 @@ synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: CALOHA:TS-0060 xref: FMA:54537 -xref: ZFA:0009075 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009075 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000126 ! macroglial cell property_value: RO:0002175 NCBITaxon:9606 @@ -597,9 +600,8 @@ subset: eye_upper_slim subset: human_reference_atlas xref: CALOHA:TS-0172 xref: FMA:70614 -xref: ZFA:0009079 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009079 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell -is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0001985 ! corneal endothelium relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell property_value: RO:0002175 NCBITaxon:9606 @@ -609,7 +611,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -633,7 +635,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -645,7 +647,7 @@ def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 -xref: ZFA:0009090 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009090 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -661,7 +663,7 @@ xref: CALOHA:TS-0613 xref: FMA:70545 xref: MESH:D008544 xref: VHOG:0001679 -xref: ZFA:0009091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome @@ -705,14 +707,14 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -728,7 +730,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -754,20 +756,20 @@ def: "A cell specialized to detect and transduce light." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 -xref: FBbt:00004211 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 -xref: ZFA:0009127 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -775,21 +777,21 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -801,7 +803,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -813,7 +815,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -823,7 +825,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -872,7 +874,7 @@ def: "Any photoreceptor cell that is part of some eye." [FBC:Autogenerated] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas -xref: ZFA:0009154 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye @@ -883,7 +885,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000293 name: structural cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] -xref: ZFA:0005745 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005745 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -904,7 +906,7 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -915,7 +917,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -925,7 +927,7 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -934,7 +936,7 @@ name: glioblast (sensu Vertebrata) def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] synonym: "spongioblast" EXACT [] xref: FMA:70564 -xref: ZFA:0009169 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000030 ! glioblast is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell @@ -943,7 +945,7 @@ is_a: CL:0011026 ! progenitor cell id: CL:0000342 name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] -xref: ZFA:0009170 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata @@ -953,7 +955,7 @@ id: CL:0000347 name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim -xref: ZFA:0009174 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera @@ -965,7 +967,7 @@ id: CL:0000348 name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim -xref: ZFA:0009175 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid @@ -997,7 +999,7 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1006,7 +1008,7 @@ name: CNS interneuron def: "An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. subset: human_reference_atlas -xref: ZFA:0009191 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009191 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000099 ! interneuron @@ -1017,7 +1019,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1028,7 +1030,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -1041,7 +1043,7 @@ def: "A neuron which conveys sensory information centrally from the periphery." subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 -xref: ZFA:0009238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -1049,7 +1051,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000529 name: pigmented epithelial cell subset: cellxgene_subset -xref: ZFA:0009241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000710 ! neurecto-epithelial cell [Term] @@ -1063,16 +1065,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1082,7 +1084,7 @@ def: "A cell that originates from the neural crest and differentiates into a pig comment: Derived from UBERON:0002342 neural crest. xref: BTO:0003217 xref: FMA:83377 -xref: ZFA:0009249 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -1141,7 +1143,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -1162,7 +1164,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -1275,7 +1277,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -1318,7 +1320,7 @@ synonym: "ACs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "amacrine neuron" EXACT [] xref: BTO:0004044 xref: FMA:67766 -xref: ZFA:0009255 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009255 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -1333,7 +1335,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1355,7 +1357,7 @@ synonym: "cone" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 -xref: ZFA:0009262 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009262 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -1371,7 +1373,7 @@ synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: CALOHA:TS-0173 xref: FMA:70551 -xref: ZFA:0009264 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009264 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell @@ -1389,7 +1391,7 @@ synonym: "rod" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 -xref: ZFA:0009275 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009275 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -1405,7 +1407,7 @@ synonym: "Muller cell" EXACT MISSPELLING [doi:10.21769/BioProtoc.4179] synonym: "Muller glia" EXACT [] synonym: "Müller cell" EXACT [] xref: BTO:0003064 -xref: ZFA:0009280 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009280 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000681 ! radial glial cell is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -1417,9 +1419,9 @@ name: glutamatergic neuron def: "A neuron that is capable of some neurotansmission by glutamate secretion." [] subset: cellxgene_subset subset: human_reference_atlas -xref: FBbt:00100291 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006829 -xref: ZFA:0009290 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009290 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -1432,7 +1434,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1446,7 +1448,7 @@ def: "A cell present in the developing CNS. Functions as both a precursor cell a comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life. subset: cellxgene_subset synonym: "forebrain radial glial cell" NARROW [] -xref: ZFA:0009292 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009292 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell relationship: RO:0002202 CL:0000710 ! develops from neurecto-epithelial cell @@ -1470,7 +1472,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1490,7 +1492,7 @@ synonym: "RGCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 -xref: ZFA:0009310 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009310 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) relationship: RO:0002100 UBERON:0000966 ! has soma location retina property_value: RO:0002175 NCBITaxon:9606 @@ -1506,7 +1508,7 @@ synonym: "HC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] xref: BTO:0004120 -xref: ZFA:0009315 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron relationship: RO:0002100 UBERON:0003902 ! has soma location retinal neural layer property_value: RO:0002175 NCBITaxon:9606 @@ -1521,7 +1523,7 @@ subset: human_reference_atlas synonym: "BC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "BCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "BPs" RELATED OMO:0003004 [GSE137537] -xref: ZFA:0009318 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009318 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000103 ! bipolar neuron is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0008028 ! visual system neuron @@ -1539,7 +1541,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1556,7 +1558,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -1571,7 +1573,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -1617,7 +1619,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -1665,7 +1667,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1685,7 +1687,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1699,7 +1701,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1713,7 +1715,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1721,12 +1723,12 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1735,12 +1737,12 @@ name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1755,7 +1757,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1764,7 +1766,7 @@ name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:31:08Z [Term] @@ -1776,7 +1778,7 @@ xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell relationship: part_of UBERON:0000965 ! lens of camera-type eye -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:38:03Z [Term] @@ -1788,7 +1790,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1803,8 +1805,8 @@ synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T04:09:27Z [Term] @@ -1820,8 +1822,8 @@ synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T04:09:31Z [Term] @@ -1835,7 +1837,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1846,12 +1848,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1861,9 +1863,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1879,8 +1881,8 @@ is_a: CL:0000005 ! neural crest derived fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T01:57:40Z [Term] @@ -1893,7 +1895,7 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:25:32Z [Term] @@ -1910,7 +1912,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1918,9 +1920,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1934,8 +1936,8 @@ is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium relationship: part_of UBERON:0002506 ! iris epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:28:52Z [Term] @@ -1950,8 +1952,8 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T03:28:27Z [Term] @@ -1970,8 +1972,8 @@ intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T03:37:09Z [Term] @@ -1980,7 +1982,7 @@ name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] is_a: CL:0000048 ! multi fate stem cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T02:38:01Z [Term] @@ -1988,7 +1990,7 @@ id: CL:0005000 name: spinal cord interneuron def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. -xref: ZFA:0000778 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0000778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000402 {is_inferred="true"} ! CNS interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002240 ! has soma location spinal cord @@ -1998,11 +2000,11 @@ relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2022,7 +2024,7 @@ is_a: CL:0000988 ! hematopoietic cell id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -2048,7 +2050,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-09T19:12:36Z [Term] @@ -2098,7 +2100,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011104 @@ -2130,7 +2132,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2141,7 +2143,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2152,7 +2154,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2189,7 +2191,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system relationship: RO:0002100 UBERON:0001017 ! has soma location central nervous system -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:43Z [Term] @@ -2200,8 +2202,8 @@ subset: eye_upper_slim synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4033015 @@ -2215,15 +2217,15 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-03-02T14:38:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-03-02T14:38:32Z" xsd:dateTime [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -3313,7 +3315,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3832,7 +3833,7 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -3847,7 +3848,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -3860,7 +3861,7 @@ relationship: results_in_assembly_of GO:0042995 ! cell projection id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -4338,7 +4339,7 @@ is_a: GO:0008150 ! biological_process id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -4356,7 +4357,7 @@ relationship: part_of CL:0000000 ! cell id: GO:0043005 name: neuron projection namespace: cellular_component -def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, PMID:3077060] subset: goslim_pir synonym: "nerve fiber" RELATED [GOC:dph] synonym: "neurite" NARROW [] @@ -4618,13 +4619,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -5094,7 +5096,7 @@ creation_date: 2013-12-18T14:04:32Z id: GO:0051649 name: establishment of localization in cell namespace: biological_process -def: "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] +def: "Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] synonym: "establishment of intracellular localization" NARROW [] synonym: "establishment of localisation in cell" EXACT [GOC:mah] @@ -5345,20 +5347,6 @@ relationship: results_in_assembly_of GO:0043226 ! organelle created_by: mah creation_date: 2009-09-15T03:00:51Z -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071826 name: protein-RNA complex organization @@ -5786,27 +5774,6 @@ relationship: has_target_start_location GO:0005622 ! intracellular anatomical st created_by: pg creation_date: 2019-05-22T11:20:45Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1903047 name: mitotic cell cycle process @@ -6528,7 +6495,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -6538,7 +6505,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6550,7 +6517,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6561,7 +6528,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -6571,7 +6538,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6581,7 +6548,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6590,7 +6557,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6603,7 +6570,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6614,7 +6581,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6624,7 +6591,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6637,7 +6604,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -6648,7 +6615,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6657,7 +6624,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6667,7 +6634,7 @@ namespace: quality def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z [Term] @@ -6699,7 +6666,7 @@ xref: ILX:0101312 xref: ilxtr:BipolarPhenotype xref: nifext:2 is_a: PATO:0070027 ! bitufted dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070027 @@ -6708,7 +6675,7 @@ namespace: quality def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -6750,6 +6717,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -7099,6 +7069,15 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -7129,6 +7108,18 @@ intersection_of: PR:000000001 ! protein intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -7206,7 +7197,7 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7221,7 +7212,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7305,8 +7296,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000047 @@ -7362,7 +7353,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7528,7 +7519,7 @@ is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -7573,7 +7564,7 @@ xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string [Term] @@ -7726,7 +7717,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -7806,7 +7797,7 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005099 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NLX:147821 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection @@ -7859,7 +7850,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -7883,7 +7874,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -7942,7 +7933,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -7965,7 +7956,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -8025,7 +8016,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8060,7 +8051,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8088,7 +8079,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8113,7 +8104,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8150,7 +8141,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -8204,7 +8195,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8248,7 +8239,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8284,7 +8275,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8304,7 +8295,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -8331,7 +8322,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8366,7 +8357,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8399,7 +8390,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8420,7 +8411,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -8449,7 +8440,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000488 @@ -8566,7 +8557,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -8587,7 +8578,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -8607,7 +8598,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8641,7 +8632,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8659,7 +8650,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8679,7 +8670,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8696,8 +8687,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8723,7 +8714,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8740,7 +8731,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -8763,7 +8754,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8776,7 +8767,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -8891,9 +8882,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -8930,7 +8921,7 @@ xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 -xref: FBbt:00005095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:50801 xref: GAID:571 xref: galen:Brain @@ -8959,8 +8950,8 @@ relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous s relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -8978,7 +8969,7 @@ is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: RO:0000086 PATO:0002124 ! has quality laminar -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] @@ -9029,7 +9020,7 @@ intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI [Term] id: UBERON:0000964 @@ -9077,7 +9068,7 @@ relationship: RO:0002202 UBERON:0004348 ! develops from optic eminence relationship: RO:0002202 UBERON:0005427 ! develops from corneal primordium relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -9177,7 +9168,7 @@ relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region relationship: RO:0002202 UBERON:0003072 {source="EHDAA2"} ! develops from optic cup -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6656 property_value: RO:0002175 NCBITaxon:9606 @@ -9199,7 +9190,7 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -9271,7 +9262,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9321,7 +9312,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -9360,7 +9351,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -9386,7 +9377,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9414,8 +9405,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -9446,7 +9437,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9485,7 +9476,7 @@ synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 -xref: FBbt:00005100 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005100 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle @@ -9537,7 +9528,7 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007692 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9552,7 +9543,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001048 @@ -9571,7 +9562,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -9618,7 +9609,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9634,7 +9625,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9695,7 +9686,7 @@ intersection_of: has_part CL:0000192 ! smooth muscle cell relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber relationship: RO:0002473 CL:0000192 ! composed primarily of smooth muscle cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI [Term] id: UBERON:0001136 @@ -9727,7 +9718,7 @@ intersection_of: part_of UBERON:0000042 ! serous membrane intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm relationship: part_of UBERON:0000042 ! serous membrane relationship: RO:0002473 CL:0000077 {source="FMA"} ! composed primarily of mesothelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI [Term] id: UBERON:0001137 @@ -9752,7 +9743,7 @@ xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] id: UBERON:0001434 @@ -9833,7 +9824,7 @@ xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head relationship: has_part UBERON:0000165 ! mouth relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] id: UBERON:0001555 @@ -9857,7 +9848,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -9901,7 +9892,7 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -9964,7 +9955,7 @@ relationship: capable_of GO:0060082 ! eye blink reflex relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye relationship: protects UBERON:0010409 ! ocular surface region relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI [Term] id: UBERON:0001766 @@ -9995,7 +9986,7 @@ xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001768 @@ -10029,7 +10020,7 @@ relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI property_value: IAO:0000116 "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} @@ -10118,7 +10109,7 @@ intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10154,7 +10145,7 @@ relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball relationship: RO:0000086 PATO:0000963 ! has quality opaque relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10193,7 +10184,7 @@ relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10237,7 +10228,7 @@ relationship: overlaps UBERON:0001802 {source="Wikipedia"} ! posterior segment o relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: IAO:0000116 "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -10276,7 +10267,7 @@ relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea relationship: part_of UBERON:0000964 ! cornea relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI [Term] id: UBERON:0001778 @@ -10381,7 +10372,7 @@ relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor la relationship: adjacent_to UBERON:0003902 ! retinal neural layer relationship: has_part GO:0048770 ! pigment granule relationship: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10412,7 +10403,7 @@ is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001788 ! outer limiting layer of retina relationship: has_part CL:0000287 {source="ZFA"} ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001788 @@ -10602,7 +10593,7 @@ relationship: adjacent_to UBERON:0001793 ! nerve fiber layer of retina relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer relationship: RO:0002473 CL:0000740 ! composed primarily of retinal ganglion cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10719,7 +10710,7 @@ relationship: overlaps CL:0000740 ! retinal ganglion cell relationship: overlaps CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001796 @@ -10750,7 +10741,7 @@ is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid relationship: part_of UBERON:0001766 ! anterior chamber of eyeball relationship: RO:0002433 UBERON:0001766 ! contributes to morphology of anterior chamber of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001797 @@ -10785,7 +10776,7 @@ is_a: UBERON:0006312 ! ocular refractive media relationship: part_of UBERON:0001798 ! vitreous body relationship: RO:0000086 PATO:0000964 ! has quality transparent relationship: RO:0001025 UBERON:0005606 ! located in hyaloid cavity -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001798 @@ -10808,7 +10799,7 @@ is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball relationship: RO:0002254 UBERON:0002346 ! has developmental contribution from neurectoderm relationship: RO:0002473 UBERON:0001797 ! composed primarily of vitreous humor -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: IAO:0000116 "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string [Term] @@ -10865,7 +10856,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI [Term] id: UBERON:0001802 @@ -10893,7 +10884,7 @@ is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001811 @@ -10930,7 +10921,7 @@ relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10976,7 +10967,7 @@ disjoint_from: UBERON:0002298 ! brainstem relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0006240 ! immediate transformation of future forebrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11026,7 +11017,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre relationship: RO:0002254 UBERON:0003849 ! has developmental contribution from mesencephalic neural crest relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0009616 {source="Bgee:AN"} ! immediate transformation of presumptive midbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI property_value: IAO:0000116 "developmental relationships need revised" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11089,7 +11080,7 @@ relationship: part_of UBERON:0001890 ! forebrain relationship: RO:0002254 UBERON:0003851 ! has developmental contribution from diencephalon neural crest relationship: RO:0002433 UBERON:0001890 ! contributes to morphology of forebrain relationship: RO:0002495 UBERON:0006222 ! immediate transformation of future diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001896 @@ -11144,7 +11135,7 @@ relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11189,9 +11180,9 @@ relationship: part_of UBERON:0002104 ! visual system relationship: part_of UBERON:0003931 ! diencephalic white matter relationship: RO:0002134 UBERON:0000966 ! innervates retina relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11235,7 +11226,7 @@ is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem relationship: RO:0002202 UBERON:0010285 {source="ZFA"} ! develops from midbrain basal plate -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11321,7 +11312,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11357,7 +11348,7 @@ intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0000964 ! cornea relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11420,7 +11411,7 @@ xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002028 @@ -11466,7 +11457,7 @@ relationship: overlaps UBERON:0002298 ! brainstem relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} property_value: RO:0002175 NCBITaxon:9606 @@ -11488,7 +11479,7 @@ is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11510,7 +11501,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11718,8 +11709,8 @@ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11782,8 +11773,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002240 @@ -11844,9 +11835,9 @@ relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11892,7 +11883,7 @@ relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum relationship: RO:0002150 UBERON:0002240 ! continuous with spinal cord relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI [Term] id: UBERON:0002316 @@ -11929,8 +11920,8 @@ xref: Wikipedia:White_matter xref: ZFA:0001682 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: RO:0002473 UBERON:0006135 ! composed primarily of myelinated nerve fiber -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -11954,7 +11945,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12011,7 +12002,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12052,7 +12043,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -12094,8 +12085,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12118,7 +12109,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12296,7 +12287,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -12507,7 +12498,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003071 @@ -12604,7 +12595,7 @@ intersection_of: RO:0002387 UBERON:0000965 ! has potential to develop into lens relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye relationship: RO:0002256 UBERON:0004128 ! developmentally induced by optic vesicle relationship: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -12639,7 +12630,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003076 @@ -12684,7 +12675,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003080 @@ -12733,7 +12724,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -12783,7 +12774,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003098 @@ -12811,7 +12802,7 @@ is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034705 {source="EHDAA2"} ! developing neuroepithelium relationship: part_of UBERON:0001894 ! diencephalon relationship: RO:0002202 UBERON:0003072 ! develops from optic cup -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003099 @@ -12897,7 +12888,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -13203,7 +13194,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -13402,7 +13393,7 @@ relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye relationship: RO:0002202 UBERON:0002346 {source="GO-def"} ! develops from neurectoderm relationship: RO:0002202 UBERON:0003071 {source="ZFA"} ! develops from eye primordium relationship: RO:0002256 UBERON:0004880 ! developmentally induced by chordamesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI [Term] id: UBERON:0004139 @@ -13697,8 +13688,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13791,7 +13782,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -13915,7 +13906,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -13931,7 +13922,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -14046,7 +14037,7 @@ synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 -xref: FBbt:00007060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83115 is_a: UBERON:0000061 ! anatomical structure relationship: RO:0002473 GO:0005575 ! composed primarily of cellular_component @@ -14181,7 +14172,7 @@ xref: VHOG:0000456 xref: Wikipedia:Myelencephalon is_a: UBERON:0004733 ! segmental subdivision of hindbrain relationship: RO:0002495 UBERON:0010096 ! immediate transformation of future myelencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0005291 @@ -14204,7 +14195,7 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000970 ! eye @@ -14235,7 +14226,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -14471,7 +14462,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -15217,7 +15208,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15420,7 +15411,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -15592,11 +15583,11 @@ xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010912 @@ -15658,7 +15649,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -15948,7 +15939,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -16185,7 +16176,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -16276,8 +16267,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Typedef] id: BFO:0000067 @@ -17352,8 +17343,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17361,8 +17352,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17371,8 +17362,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -17523,16 +17514,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -17541,6 +17536,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -17558,6 +17554,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -17776,6 +17773,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -18234,18 +18232,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/src/ontology/subsets/eye_upper_slim.owl b/src/ontology/subsets/eye_upper_slim.owl index a35d2da8e..96eb56261 100644 --- a/src/ontology/subsets/eye_upper_slim.owl +++ b/src/ontology/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4516,6 +4522,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4527,6 +4535,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4537,6 +4546,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4549,6 +4559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4567,6 +4578,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4596,6 +4608,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4704,6 +4717,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4715,6 +4729,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4726,6 +4741,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -5685,15 +5701,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - @@ -5710,17 +5725,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -6017,7 +6025,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -6225,7 +6238,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -10003,7 +10015,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -10046,7 +10058,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10085,7 +10097,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -10129,7 +10141,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cell derived from mesoderm or mesenchyme. - 2010-06-29T03:49:14Z + 2010-06-29T03:49:14Z FMA:69076 ZFA:0009388 epithelial mesenchymal cell @@ -10157,7 +10169,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -10184,7 +10196,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cells derived from general body ectoderm and ectoderm placodes. - 2010-08-26T08:31:08Z + 2010-08-26T08:31:08Z FMA:70556 general ecto-epithelial cell @@ -10210,7 +10222,7 @@ radial glial cells acting as neural progenitors throughout life. A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. - 2010-09-07T10:38:03Z + 2010-09-07T10:38:03Z FMA:70950 vertebrate lens cell @@ -10248,7 +10260,7 @@ radial glial cells acting as neural progenitors throughout life. A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -10274,7 +10286,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. - 2010-09-13T04:09:27Z + 2010-09-13T04:09:27Z FMA:70606 PE cell @@ -10317,7 +10329,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of non-pigmented ciliary epithelium. This cell type participates in aqueous humor formation by releasing solute, principally sodium and chloride ions received from pigmented epithelial cells via gap junctions, into the aqueous humor of the eye. - 2010-09-13T04:09:31Z + 2010-09-13T04:09:31Z FMA:70607 NPE cell nonpigmented ciliary epithelial cell @@ -10378,7 +10390,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -10417,7 +10429,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -10447,7 +10459,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -10493,7 +10505,7 @@ radial glial cells acting as neural progenitors throughout life. A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. - 2010-09-22T01:57:40Z + 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte @@ -10535,7 +10547,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. - 2010-12-03T03:25:32Z + 2010-12-03T03:25:32Z retinal melanocyte @@ -10572,7 +10584,7 @@ radial glial cells acting as neural progenitors throughout life. A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -10596,7 +10608,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -10641,7 +10653,7 @@ radial glial cells acting as neural progenitors throughout life. A pigment cell located in the epithelium of the iris. - 2011-03-01T05:28:52Z + 2011-03-01T05:28:52Z iris pigment epithelial cell @@ -10686,7 +10698,7 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. - 2011-03-06T03:28:27Z + 2011-03-06T03:28:27Z @@ -10739,7 +10751,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. - 2011-03-06T03:37:09Z + 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 @@ -10768,7 +10780,7 @@ radial glial cells acting as neural progenitors throughout life. A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. - 2011-08-16T02:38:01Z + 2011-08-16T02:38:01Z retinal progenitor cell @@ -10847,7 +10859,7 @@ radial glial cells acting as neural progenitors throughout life. Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -11230,7 +11242,7 @@ plexiform layer. Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -11266,7 +11278,7 @@ plexiform layer. Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -11301,7 +11313,7 @@ plexiform layer. Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -11433,8 +11445,8 @@ plexiform layer. Any neuron that is part of a central nervous system. - - 2014-06-25T01:17:43Z + + 2014-06-25T01:17:43Z CL:2000029 central nervous system neuron @@ -11585,7 +11597,6 @@ plexiform layer. Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 - Reactome:69278 @@ -14135,7 +14146,6 @@ plexiform layer. - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -15475,7 +15485,7 @@ plexiform layer. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -15527,7 +15537,7 @@ plexiform layer. Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:18391171 @@ -15562,7 +15572,6 @@ plexiform layer. ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -16876,7 +16885,7 @@ plexiform layer. A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -16920,7 +16929,7 @@ plexiform layer. A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:3077060 @@ -17606,6 +17615,7 @@ plexiform layer. The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite primary metabolism biological_process GO:0044238 @@ -17621,7 +17631,6 @@ plexiform layer. The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators - http://www.metacyc.org @@ -18884,7 +18893,7 @@ plexiform layer. - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. + Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell @@ -18897,7 +18906,7 @@ plexiform layer. - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. + Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph @@ -19547,31 +19556,6 @@ plexiform layer. - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism - biological_process - GO:0071704 - - organic substance metabolic process - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - GOC:mah - - - - @@ -20845,63 +20829,6 @@ plexiform layer. - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -23041,6 +22968,14 @@ plexiform layer. + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -23963,6 +23898,39 @@ plexiform layer. + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -24067,6 +24035,58 @@ plexiform layer. + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -25140,7 +25160,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) EHDAA2:0001968 @@ -25163,7 +25183,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -25176,7 +25196,7 @@ plexiform layer. - + EHDAA2 @@ -25525,7 +25545,7 @@ plexiform layer. - + @@ -25561,14 +25581,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -25976,15 +25996,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -26021,34 +26041,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -27133,7 +27153,7 @@ plexiform layer. - + @@ -27175,14 +27195,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27704,7 +27724,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27739,14 +27759,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27786,7 +27806,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27821,14 +27841,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27869,7 +27889,7 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27910,14 +27930,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28105,7 +28125,7 @@ plexiform layer. - + @@ -28167,14 +28187,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -28284,7 +28304,7 @@ plexiform layer. - + @@ -28356,14 +28376,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -28405,7 +28425,7 @@ plexiform layer. - + @@ -28424,7 +28444,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -28483,11 +28503,11 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -28500,13 +28520,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -28756,9 +28776,9 @@ plexiform layer. - - + + @@ -28842,34 +28862,34 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + MA - + MA - + FMA-isa @@ -29046,10 +29066,10 @@ plexiform layer. - - + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -29097,44 +29117,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -29189,8 +29209,8 @@ plexiform layer. - - + + @@ -29222,24 +29242,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29628,7 +29648,7 @@ plexiform layer. - + @@ -29678,14 +29698,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29751,7 +29771,7 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29796,7 +29816,7 @@ plexiform layer. central nervous system - + @@ -29810,7 +29830,7 @@ plexiform layer. - + Bgee:AN @@ -30463,7 +30483,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -30488,14 +30508,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -30791,7 +30811,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30828,14 +30848,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -30890,7 +30910,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -30913,7 +30933,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -30932,7 +30952,7 @@ plexiform layer. - + FMA @@ -31050,7 +31070,7 @@ plexiform layer. - + @@ -31096,14 +31116,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31369,7 +31389,7 @@ plexiform layer. - + @@ -31408,14 +31428,14 @@ plexiform layer. iris - + - + XAO @@ -31469,7 +31489,7 @@ plexiform layer. - + @@ -31518,14 +31538,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31613,15 +31633,15 @@ plexiform layer. - - + + - + @@ -31656,34 +31676,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31725,7 +31745,7 @@ plexiform layer. - + @@ -31763,14 +31783,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31808,14 +31828,14 @@ plexiform layer. - + - + @@ -31876,24 +31896,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32086,9 +32106,9 @@ plexiform layer. - - + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32108,15 +32128,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32129,19 +32149,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32257,7 +32277,7 @@ plexiform layer. - + @@ -32315,14 +32335,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32398,7 +32418,7 @@ plexiform layer. - + @@ -32430,14 +32450,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -32930,7 +32950,7 @@ plexiform layer. - + @@ -32986,7 +33006,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -32999,7 +33019,7 @@ plexiform layer. - + FMA @@ -33053,7 +33073,7 @@ plexiform layer. - + @@ -33108,14 +33128,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33805,7 +33825,7 @@ plexiform layer. - + @@ -33837,14 +33857,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -33888,7 +33908,7 @@ plexiform layer. - + @@ -33918,14 +33938,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -33962,9 +33982,9 @@ plexiform layer. - - + + @@ -34012,15 +34032,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34033,19 +34053,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34203,7 +34223,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34249,14 +34269,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34727,7 +34747,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34766,14 +34786,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -34941,8 +34961,8 @@ plexiform layer. - - + + @@ -34955,7 +34975,7 @@ plexiform layer. - + @@ -35009,34 +35029,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35365,7 +35385,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35408,14 +35428,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -36046,7 +36066,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36068,14 +36088,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -36279,7 +36299,7 @@ plexiform layer. - + @@ -36353,14 +36373,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - + ZFA @@ -36815,9 +36835,9 @@ plexiform layer. - - + + @@ -36865,15 +36885,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -36892,19 +36912,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36944,8 +36964,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -36983,11 +37003,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -37000,13 +37020,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37068,22 +37088,22 @@ plexiform layer. - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37116,45 +37136,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37440,7 +37460,7 @@ plexiform layer. - + @@ -37493,14 +37513,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37540,8 +37560,8 @@ plexiform layer. - - + + @@ -37567,11 +37587,11 @@ plexiform layer. iris epithelium - + - + @@ -37584,13 +37604,13 @@ plexiform layer. - + MA - + MP @@ -37729,7 +37749,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37746,7 +37766,7 @@ plexiform layer. cranial placode - + @@ -37759,7 +37779,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -37959,7 +37979,7 @@ plexiform layer. - + @@ -37972,7 +37992,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38001,24 +38021,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38140,7 +38160,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38163,14 +38183,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38337,7 +38357,7 @@ plexiform layer. - + @@ -38374,7 +38394,7 @@ plexiform layer. eye primordium - + @@ -38387,7 +38407,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38437,8 +38457,8 @@ plexiform layer. - - + + @@ -38466,24 +38486,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38539,7 +38559,7 @@ plexiform layer. - + @@ -38577,7 +38597,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38590,7 +38610,7 @@ plexiform layer. - + ZFA @@ -38629,9 +38649,9 @@ plexiform layer. - - + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38660,34 +38680,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38762,7 +38782,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38788,7 +38808,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38801,7 +38821,7 @@ plexiform layer. - + Bgee:AN @@ -38877,7 +38897,7 @@ plexiform layer. - + @@ -38917,7 +38937,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38930,7 +38950,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -38980,15 +39000,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39005,15 +39025,15 @@ plexiform layer. heart primordium - + - + - + @@ -39026,19 +39046,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39067,8 +39087,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39092,11 +39112,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -39115,13 +39135,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39442,7 +39462,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39454,14 +39474,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40236,7 +40256,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40251,14 +40271,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40351,7 +40371,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40382,14 +40402,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40642,7 +40662,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40659,7 +40679,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40672,7 +40692,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41074,9 +41094,9 @@ plexiform layer. - - + + @@ -41108,34 +41128,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41231,8 +41251,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41244,24 +41264,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41314,7 +41334,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41333,14 +41353,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41417,7 +41437,7 @@ plexiform layer. - + @@ -41433,14 +41453,14 @@ plexiform layer. eye muscle - + - + MA @@ -41623,7 +41643,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41652,14 +41672,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -42409,7 +42429,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42423,14 +42443,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42457,7 +42477,7 @@ plexiform layer. - + @@ -42496,14 +42516,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -43355,7 +43375,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43376,14 +43396,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43441,7 +43461,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43457,14 +43477,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -43979,7 +43999,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -43987,7 +44007,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44006,7 +44026,7 @@ plexiform layer. - + ZFA @@ -44029,7 +44049,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44047,14 +44067,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44244,7 +44264,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44254,7 +44274,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44273,7 +44293,7 @@ plexiform layer. - + AEO-modified-relation @@ -44330,8 +44350,8 @@ plexiform layer. - - + + @@ -44348,11 +44368,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44365,13 +44385,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44613,7 +44633,7 @@ plexiform layer. - + @@ -44636,14 +44656,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44819,7 +44839,7 @@ plexiform layer. - + @@ -44843,14 +44863,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -44887,7 +44907,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44901,7 +44921,7 @@ plexiform layer. notochordal plate - + @@ -44914,7 +44934,7 @@ plexiform layer. - + EHDAA2 @@ -44942,7 +44962,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44959,14 +44979,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -46007,8 +46027,8 @@ plexiform layer. - - + + @@ -46034,24 +46054,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46102,7 +46122,7 @@ plexiform layer. - + @@ -46121,14 +46141,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46274,7 +46294,7 @@ plexiform layer. - + @@ -46300,7 +46320,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46316,7 +46336,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46398,7 +46418,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46406,7 +46426,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46419,7 +46439,7 @@ plexiform layer. - + Obol @@ -46494,7 +46514,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46502,7 +46522,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46515,7 +46535,7 @@ plexiform layer. - + AEO @@ -46754,7 +46774,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46764,14 +46784,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46799,7 +46819,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46816,14 +46836,14 @@ plexiform layer. vascular system - + - + MA @@ -46944,7 +46964,7 @@ plexiform layer. - + @@ -46961,14 +46981,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47064,7 +47084,7 @@ plexiform layer. - + @@ -47080,14 +47100,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47120,14 +47140,14 @@ plexiform layer. - + - + @@ -47152,24 +47172,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47215,7 +47235,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47223,14 +47243,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47253,7 +47273,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47263,14 +47283,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47326,14 +47346,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47346,7 +47366,7 @@ plexiform layer. - + EHDAA2 @@ -47487,7 +47507,7 @@ plexiform layer. - + @@ -47510,14 +47530,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47558,8 +47578,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47573,11 +47593,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47590,13 +47610,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47625,7 +47645,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47634,14 +47654,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -47944,8 +47964,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -47957,11 +47977,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -47974,13 +47994,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48041,7 +48061,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48051,7 +48071,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48064,7 +48084,7 @@ plexiform layer. - + cjm @@ -48186,7 +48206,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48196,14 +48216,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48465,7 +48485,7 @@ plexiform layer. - + @@ -48507,7 +48527,7 @@ plexiform layer. anterior uvea - + @@ -48520,7 +48540,7 @@ plexiform layer. - + MP @@ -49313,7 +49333,7 @@ plexiform layer. - + @@ -49336,7 +49356,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49349,7 +49369,7 @@ plexiform layer. - + AEO @@ -50339,5 +50359,5 @@ plexiform layer. - + diff --git a/src/ontology/subsets/eye_upper_slim.tsv b/src/ontology/subsets/eye_upper_slim.tsv index 1d366ed5e..f6a93c692 100644 --- a/src/ontology/subsets/eye_upper_slim.tsv +++ b/src/ontology/subsets/eye_upper_slim.tsv @@ -1,315 +1,315 @@ ?x ?label -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1001 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1016 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1022 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1031 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1037 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1043 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1051 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1058 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1065 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1074 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+_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid73 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid760 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid779 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid795 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid802 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid813 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid819 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid836 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid842 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid851 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid861 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid909 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid959 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid969 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid976 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid983 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid990 "cell" "neural crest derived fibroblast" "neuronal receptor cell" @@ -682,7 +682,6 @@ _:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid990 "extracellular exosome" "anchoring junction" "organelle assembly" - "organic substance metabolic process" "protein-RNA complex organization" "cellular component organization or biogenesis" "cell periphery" @@ -717,7 +716,6 @@ _:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid990 "mitotic nuclear division" "extracellular vesicle biogenesis" "export from cell" - "organic substance biosynthetic process" "mitotic cell cycle process" "regulation of blood circulation" "extracellular vesicle" @@ -840,9 +838,11 @@ _:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid990 "lymphocyte antigen 76 (mouse)" "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "eukaryotic protein" + "protein-containing molecular entity" "processual entity" "camera-type eye" "sense organ" diff --git a/src/ontology/subsets/general_cell_types_upper_slim.json b/src/ontology/subsets/general_cell_types_upper_slim.json index effd7a8d6..a7dcbb071 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.json +++ b/src/ontology/subsets/general_cell_types_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -3182,62 +3029,6 @@ "val" : "CALOHA:TS-2109" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000323", "lbl" : "lytic vacuole", @@ -3405,6 +3196,24 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0001677", + "lbl" : "formation of translation initiation ternary complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", + "xrefs" : [ "GOC:hjd" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "translation initiation ternary complex assembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0001704", "lbl" : "formation of primary germ layer", @@ -4583,6 +4392,144 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006412", + "lbl" : "translation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein anabolism" + }, { + "pred" : "hasExactSynonym", + "val" : "protein biosynthesis" + }, { + "pred" : "hasExactSynonym", + "val" : "protein biosynthetic process" + }, { + "pred" : "hasExactSynonym", + "val" : "protein formation" + }, { + "pred" : "hasExactSynonym", + "val" : "protein synthesis" + }, { + "pred" : "hasExactSynonym", + "val" : "protein translation" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Translation_(genetics)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006416" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006453" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043037" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006413", + "lbl" : "translational initiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.", + "xrefs" : [ "ISBN:019879276X" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "biopolymerisation" + }, { + "pred" : "hasBroadSynonym", + "val" : "biopolymerization" + }, { + "pred" : "hasBroadSynonym", + "val" : "protein synthesis initiation" + }, { + "pred" : "hasExactSynonym", + "val" : "translation initiation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006440" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006454" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006414", + "lbl" : "translational elongation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.", + "xrefs" : [ "GOC:ems" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "protein synthesis elongation" + }, { + "pred" : "hasExactSynonym", + "val" : "translation elongation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006442" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006455" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006415", + "lbl" : "translational termination", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).", + "xrefs" : [ "GOC:hjd", "ISBN:019879276X" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "protein synthesis termination" + }, { + "pred" : "hasExactSynonym", + "val" : "translation termination" + }, { + "pred" : "hasExactSynonym", + "val" : "translational complex disassembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006443" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006456" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006810", "lbl" : "transport", @@ -4646,7 +4593,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", + "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", "xrefs" : [ "GOC:mah", "ISBN:0716731363", "PMID:22323285" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -6074,6 +6021,59 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0019538", + "lbl" : "protein metabolic process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways involving a protein. Includes protein modification.", + "xrefs" : [ "GOC:ma" ] + }, + "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular protein metabolic process" + }, { + "pred" : "hasExactSynonym", + "val" : "cellular protein metabolism" + }, { + "pred" : "hasExactSynonym", + "val" : "protein metabolic process and modification" + }, { + "pred" : "hasExactSynonym", + "val" : "protein metabolism" + }, { + "pred" : "hasExactSynonym", + "val" : "protein metabolism and modification" + }, { + "pred" : "hasNarrowSynonym", + "val" : "multicellular organismal protein metabolic process" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Protein_metabolism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/23112" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27189" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044267" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044268" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0019724", "lbl" : "B cell mediated immunity", @@ -6148,6 +6148,35 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022411", + "lbl" : "cellular component disassembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process that results in the breakdown of a cellular component.", + "xrefs" : [ "GOC:isa_complete" ] + }, + "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cell structure disassembly" + }, { + "pred" : "hasExactSynonym", + "val" : "cellular component disassembly at cellular level" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27189" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071845" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0022414", "lbl" : "reproductive process", @@ -6197,6 +6226,79 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022607", + "lbl" : "cellular component assembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The aggregation, arrangement and bonding together of a cellular component.", + "xrefs" : [ "GOC:isa_complete" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cell structure assembly" + }, { + "pred" : "hasExactSynonym", + "val" : "cellular component assembly at cellular level" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071844" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022613", + "lbl" : "ribonucleoprotein complex biogenesis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.", + "xrefs" : [ "GOC:isa_complete", "GOC:mah" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "RNA-protein complex biogenesis", + "xrefs" : [ "GOC:mah" ] + }, { + "pred" : "hasExactSynonym", + "val" : "ribonucleoprotein complex biogenesis and assembly", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022618", + "lbl" : "protein-RNA complex assembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.", + "xrefs" : [ "GOC:jl" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "RNA-protein complex assembly" + }, { + "pred" : "hasExactSynonym", + "val" : "RNP complex assembly" + }, { + "pred" : "hasExactSynonym", + "val" : "ribonucleoprotein complex assembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0023052", "lbl" : "signaling", @@ -6305,7 +6407,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -6335,7 +6437,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -6966,6 +7068,45 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0032984", + "lbl" : "protein-containing complex disassembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The disaggregation of a protein-containing macromolecular complex into its constituent components.", + "xrefs" : [ "GOC:mah" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein complex disassembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecule complex disassembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular protein complex disassembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecule complex disassembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22580" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034623" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043241" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043624" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032991", "lbl" : "protein-containing complex", @@ -7366,7 +7507,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -7628,6 +7769,116 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0043933", + "lbl" : "protein-containing complex organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.", + "xrefs" : [ "GOC:mah" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein complex subunit organisation", + "xrefs" : [ "GOC:mah" ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein complex subunit organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecular complex organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecular complex subunit organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecular complex subunit organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex subunit organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex subunit organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "protein-containing complex subunit organization" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22580" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "mah" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-09-08T10:01:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034600" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034621" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071822" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044085", + "lbl" : "cellular component biogenesis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", + "xrefs" : [ "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular component biogenesis at cellular level" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071843" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044207", + "lbl" : "translation initiation ternary complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", + "xrefs" : [ "GOC:jl" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "translation initiation (ternary) complex" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Met-tRNA/eIF2.GTP ternary complex" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-10-22T02:38:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044237", "lbl" : "cellular metabolic process", @@ -7652,6 +7903,31 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044238", + "lbl" : "primary metabolic process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "primary metabolism" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26424" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044249", "lbl" : "cellular biosynthetic process", @@ -8881,6 +9157,58 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0065003", + "lbl" : "protein-containing complex assembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.", + "xrefs" : [ "GOC:jl" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular protein complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecule complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular protein-containing complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "chaperone activity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecule complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "protein complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "protein complex formation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22580" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006461" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034622" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043623" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0065007", "lbl" : "biological regulation", @@ -8956,34 +9284,39 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071704", - "lbl" : "organic substance metabolic process", + "id" : "http://purl.obolibrary.org/obo/GO_0071826", + "lbl" : "protein-RNA complex organization", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.", + "val" : "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolic process" + "val" : "RNA-protein complex subunit organization", + "xrefs" : [ "GOC:mah" ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein-RNA complex subunit organization", + "xrefs" : [ "GOC:mah" ] }, { "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolism" + "val" : "ribonucleoprotein complex subunit organisation", + "xrefs" : [ "GOC:mah" ] }, { "pred" : "hasExactSynonym", - "val" : "organic substance metabolism" + "val" : "ribonucleoprotein complex subunit organization" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" + "val" : "https://github.com/geneontology/go-ontology/issues/25143" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-03-08T03:32:18Z" + "val" : "2010-09-08T10:10:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9652,62 +9985,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1902105", "lbl" : "regulation of leukocyte differentiation", @@ -9796,279 +10073,71 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_2000026", - "lbl" : "regulation of multicellular organismal development", + "id" : "http://purl.obolibrary.org/obo/GO_1990904", + "lbl" : "ribonucleoprotein complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of multicellular organismal development.", - "xrefs" : [ "GOC:obol" ] + "val" : "A macromolecular complex that contains both RNA and protein molecules.", + "xrefs" : [ "GOC:krc", "GOC:vesicles" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "RNA-protein complex" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-08-05T11:25:59Z" + "pred" : "hasExactSynonym", + "val" : "RNP" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "pred" : "hasExactSynonym", + "val" : "protein-RNA complex" + }, { + "pred" : "hasNarrowSynonym", + "val" : "extracellular ribonucleoprotein complex" + }, { + "pred" : "hasNarrowSynonym", + "val" : "intracellular ribonucleoprotein complex" + } ], "xrefs" : [ { - "val" : "IAO:0000233" + "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pr" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2015-11-19T12:26:37Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0030529" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:1990903" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/GO_2000026", + "lbl" : "regulation of multicellular organismal development", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." + "val" : "Any process that modulates the frequency, rate or extent of multicellular organismal development.", + "xrefs" : [ "GOC:obol" ] }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "tb" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-08-05T11:25:59Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -10737,73 +10806,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -13411,6 +13413,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -13515,4893 +13541,6861 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "xrefs" : [ { - "val" : "RO:0000053" + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" + "val" : "protein" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000056" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000020", + "lbl" : "sense organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "An organ that is capable of transducing sensory stimulus to the nervous system.", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/549", "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "organ of sense organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory system organ", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "sensillum", + "xrefs" : [ "WBbt:0006929" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Sinnesorgan", + "xrefs" : [ "BTO:0000202" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "sensor" + } ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "AEO:0000094" + }, { + "val" : "BSA:0000121" + }, { + "val" : "BTO:0000202" + }, { + "val" : "CALOHA:TS-2043" + }, { + "val" : "EHDAA2:0001824" + }, { + "val" : "EHDAA:500" + }, { + "val" : "EMAPA:35955" + }, { + "val" : "FBbt:00005155" + }, { + "val" : "GAID:63" + }, { + "val" : "HAO:0000930" + }, { + "val" : "MA:0000017" + }, { + "val" : "MESH:D012679" + }, { + "val" : "NCIT:C33224" + }, { + "val" : "SCTID:244485009" + }, { + "val" : "UMLS:C0935626" + }, { + "val" : "VHOG:0001407" + }, { + "val" : "WBbt:0006929" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], + "xrefs" : [ { + "val" : "galen:Tube" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000043", + "lbl" : "tendon", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "Dense regular connective tissue that connects muscle to bone[VSAO].", + "xrefs" : [ "GO_REF:0000034", "VSAO:0000073", "Wikipedia:Tendon", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "sinew", + "xrefs" : [ "Wikipedia:Tendon" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tendo", + "xrefs" : [ "Wikipedia:Tendon" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000091" + }, { + "val" : "BTO:0001356" + }, { + "val" : "CALOHA:TS-1021" + }, { + "val" : "EHDAA2:0003091" + }, { + "val" : "EMAPA:35854" + }, { + "val" : "EV:0100149" + }, { + "val" : "FMA:9721" + }, { + "val" : "GAID:276" + }, { + "val" : "MA:0000115" + }, { + "val" : "MESH:D013710" + }, { + "val" : "NCIT:C13045" + }, { + "val" : "SCTID:256667004" + }, { + "val" : "UMLS:C0039508" + }, { + "val" : "VHOG:0001286" + }, { + "val" : "VSAO:0000073" + }, { + "val" : "Wikipedia:Tendon" + }, { + "val" : "XAO:0000173" + }, { + "val" : "ZFA:0005647" + }, { + "val" : "galen:Tendon" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "lbl" : "duct", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "A tubular structure that transports secreted or excreted substances.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165", "http://www.siumed.edu/~dking2/intro/glands.htm#ducts" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine gland duct" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "ducts", + "xrefs" : [ "XAO:0004000" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011123" + }, { + "val" : "FBbt:00100314" + }, { + "val" : "FMA:30320" + }, { + "val" : "NCIT:C12948" + }, { + "val" : "SCTID:91726008" + }, { + "val" : "TAO:0005171" + }, { + "val" : "UMLS:C0687028" + }, { + "val" : "Wikipedia:Duct_(anatomy)" + }, { + "val" : "XAO:0004000" + }, { + "val" : "ZFA:0005171" + }, { + "val" : "galen:Duct" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000060", + "lbl" : "anatomical wall", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.", + "xrefs" : [ "FMA:82482" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "wall" + }, { + "pred" : "hasExactSynonym", + "val" : "wall of organ", + "xrefs" : [ "FMA:82482" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ wall", + "xrefs" : [ "FMA:82482" ] + } ], + "xrefs" : [ { + "val" : "FMA:82482" + }, { + "val" : "galen:Wall" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0009915" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000061", + "lbl" : "anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "CARO:0000003" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological structure" + }, { + "pred" : "hasExactSynonym", + "val" : "connected biological structure", + "xrefs" : [ "CARO:0000003" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010825" + }, { + "val" : "AEO:0000003" + }, { + "val" : "BILA:0000003" + }, { + "val" : "CARO:0000003" + }, { + "val" : "EHDAA2:0003003" + }, { + "val" : "EMAPA:0" + }, { + "val" : "FBbt:00007001" + }, { + "val" : "FMA:305751" + }, { + "val" : "FMA:67135" + }, { + "val" : "GAID:781" + }, { + "val" : "HAO:0000003" + }, { + "val" : "MA:0003000" + }, { + "val" : "MESH:D000825" + }, { + "val" : "SCTID:362889002" + }, { + "val" : "TAO:0000037" + }, { + "val" : "TGMA:0001823" + }, { + "val" : "VHOG:0001759" + }, { + "val" : "XAO:0003000" + }, { + "val" : "ZFA:0000037" + }, { + "val" : "http://dbpedia.org/ontology/AnatomicalStructure" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001025", - "lbl" : "located in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000062", + "lbl" : "organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + "val" : "Anatomical structure that performs a specific function or group of functions [WP].", + "xrefs" : [ "Wikipedia:Organ_(anatomy)" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "anatomical unit" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "hasRelatedSynonym", + "val" : "body organ" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Located_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", - "lbl" : "2D boundary of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" - }, + "pred" : "hasRelatedSynonym", + "val" : "element", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:4" + }, { + "val" : "CARO:0020004" + }, { + "val" : "EFO:0000634" + }, { + "val" : "EMAPA:35949" + }, { + "val" : "ENVO:01000162" + }, { + "val" : "FMA:67498" + }, { + "val" : "MA:0003001" + }, { + "val" : "NCIT:C13018" + }, { + "val" : "SCTID:272625005" + }, { + "val" : "UMLS:C0178784" + }, { + "val" : "WBbt:0003760" + }, { + "val" : "Wikipedia:Organ_(anatomy)" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", - "lbl" : "has 2D boundary", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000063", + "lbl" : "organ subunit", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + "val" : "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "organ region with fixed fiat boundary", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ segment", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "segment of organ", + "xrefs" : [ "FMA:86140" ] + } ], + "xrefs" : [ { + "val" : "FMA:86140" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002005", - "lbl" : "innervated_by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002006", - "lbl" : "has synaptic terminal of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002007", - "lbl" : "bounding layer of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000064", + "lbl" : "organ part", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + "val" : "A multicellular structure that is a part of an organ.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cardinal organ part", + "xrefs" : [ "FMA:82472" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "regional part of organ", + "xrefs" : [ "BIRNLEX:16" ] + } ], "xrefs" : [ { - "val" : "RO:0002007" + "val" : "AAO:0011124" + }, { + "val" : "BIRNLEX:16" + }, { + "val" : "EFO:0000635" + }, { + "val" : "FMA:82472" + }, { + "val" : "SCTID:113343008" + }, { + "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bounding_layer_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002021", - "lbl" : "occurs across", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-7073-9172" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-07-20T17:19:37Z" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002081", - "lbl" : "before or simultaneous with", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "Primitive instance level timing relation between events" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002082", - "lbl" : "simultaneous with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000066", + "lbl" : "fully formed stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." + "val" : "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002086", - "lbl" : "ends after", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002087", - "lbl" : "immediately preceded by", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "adult stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fully formed animal stage" + }, { + "pred" : "hasExactSynonym", + "val" : "juvenile-adult stage" + } ], "xrefs" : [ { - 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"val" : "RO:0002090" + "val" : "BilaDO:0000002" + }, { + "val" : "EV:0300001" + }, { + "val" : "FBdv:00005289" + }, { + "val" : "FMA:72652" + }, { + "val" : "HsapDv:0000002" + }, { + "val" : "MmusDv:0000002" + }, { + "val" : "OGES:000000" + }, { + "val" : "OGES:000022" + }, { + "val" : "SCTID:296280003" + }, { + "val" : "WBls:0000003" + }, { + "val" : "WBls:0000092" + }, { + "val" : "WBls:0000102" + }, { + "val" : "XAO:1000012" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_precedes" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002100", - "lbl" : "has soma location", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000071", + "lbl" : "death stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." + "val" : "End of the life of an organism.", + "xrefs" : [ "XAO:0000437" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "death" + } ], + "xrefs" : [ { + "val" : "XAO:0000437" + }, { + "val" : "XtroDO:0000085" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some (\n and some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002101", - "lbl" : "fasciculates with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002102", - "lbl" : "axon synapses in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000075", + "lbl" : "subdivision of skeletal system", + "type" : "CLASS", "meta" : { "definition" : { - 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" + "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "developmental stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000105" + }, { + "val" : "EFO:0000399" + }, { + "val" : "FBdv:00007012" + }, { + "val" : "FMA:24120" + }, { + "val" : "HsapDv:0000000" + }, { + "val" : "MESH:D008018" + }, { + "val" : "MmusDv:0000000" + }, { + "val" : "OlatDv:0000010" + }, { + "val" : "PdumDv:0000090" + }, { + "val" : "WBls:0000002" + }, { + "val" : "XAO:1000000" + }, { + "val" : "ZFS:0000000" + }, { + "val" : "ZFS:0100000" + }, { + "val" : "ncithesaurus:Developmental_Stage" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002113", - "lbl" : "has presynaptic terminal in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000106", + "lbl" : "zygote stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." + "val" : "A stage at which the organism is a single cell produced by means of sexual reproduction.", + "xrefs" : [ "Wikipedia:Zygote" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "1-cell stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fertilized egg stage", + "xrefs" : [ "BTO:0000854" ] + }, { + "pred" : "hasExactSynonym", + "val" : "one cell stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fertilized egg stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "one-cell stage", + "xrefs" : [ "VHOG:0000745" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "zygote", + "xrefs" : [ "VHOG:0000745" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "zygotum", + "xrefs" : [ "Wikipedia:Zygote" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000106" + }, { + "val" : "BilaDO:0000005" + }, { + "val" : "EFO:0001322" + }, { + "val" : "EHDAA:27" + }, { + "val" : "FBdv:00005288" + }, { + "val" : "NCIT:C12601" + }, { + "val" : "PdumDv:0000100" + }, { + "val" : "VHOG:0000745" + }, { + "val" : "Wikipedia:Zygote" + }, { + "val" : "XAO:1000001" + }, { + "val" : "ZFS:0000001" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some ( that some Y?)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002120", - "lbl" : "synapsed to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " - }, - "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that some ( that some Y?)))" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002130", - "lbl" : "has synaptic terminal in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000107", + "lbl" : "cleavage stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + "val" : "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.", + "xrefs" : [ "GO:0040016", "Wikipedia:Cleavage_(embryo)" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000107" + }, { + "val" : "BilaDO:0000006" + }, { + "val" : "EFO:0001290" + }, { + "val" : "FBdv:00000054" + }, { + "val" : "MESH:D002970" + }, { + "val" : "MmusDv:0000004" + }, { + "val" : "OGES:000015" + }, { + "val" : "OGES:000020" + }, { + "val" : "PdumDv:0000200" + }, { + "val" : "Wikipedia:Cleavage_(embryo)" + }, { + "val" : "XAO:1000004" + }, { + "val" : "ZFS:0000046" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some Y?)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", - "lbl" : "overlaps", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000108", + "lbl" : "blastula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" + "val" : "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. 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This will give rise to the central nervous system.", + "xrefs" : [ "GO:0001841" ] }, + "xrefs" : [ { + "val" : "BILS:0000110" + }, { + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", - "lbl" : "shares ancestor with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." - }, - "comments" : [ "VBO calls this homologous_to" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", - "lbl" : "only in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000165", + "lbl" : "mouth", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "xrefs" : [ "Wikipedia:Mouth", "https://github.com/obophenotype/uberon/wiki/The-digestive-tract" ] }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio oralis", + "xrefs" : [ "BTO:0004698", "FMA:49184", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "cavital oralis", + "xrefs" : [ "Wikipedia:Mouth" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavitas oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavum oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth cavity", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral region", + "xrefs" : [ "EHDAA2:0001326" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral vestibule", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "rima oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "stoma" + }, { + "pred" : "hasRelatedSynonym", + "val" : "stomatodaeum", + "xrefs" : [ "VHOG:0000812" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trophic apparatus", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibule of mouth", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibulum oris", + "xrefs" : [ "BTO:0001090" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010355" + }, { + "val" : "BTO:0001090" + }, { + "val" : "BTO:0004698" + }, { + "val" : "CALOHA:TS-1315" + }, { + "val" : "EFO:0000825" + }, { + "val" : "EHDAA2:0001326" + }, { + "val" : "EHDAA:542" + }, { + "val" : "EMAPA:16262" + }, { + "val" : "FBbt:00003126" + }, { + "val" : "FMA:49184" + }, { + "val" : "GAID:75" + }, { + "val" : "MA:0000341" + }, { + "val" : "MA:0002474" + }, { + "val" : "MAT:0000038" + }, { + "val" : "MESH:D009055" + }, { + "val" : "MIAA:0000038" + }, { + "val" : "SCTID:21082005" + }, { + "val" : "TADS:0000040" + }, { + "val" : "TAO:0000547" + }, { + "val" : "TAO:0000590" + }, { + "val" : "TGMA:0000131" + }, { + "val" : "VHOG:0000280" + }, { + "val" : "VHOG:0000812" + }, { + "val" : "Wikipedia:Mouth" + }, { + "val" : "XAO:0003029" + }, { + "val" : "ZFA:0000547" + }, { + "val" : "ZFA:0000590" + }, { + "val" : "galen:Mouth" + }, { + "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/661" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", + "lbl" : "blastula", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blastula embryo", + "xrefs" : [ "BILA:0000059" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastosphere", + "xrefs" : [ "Wikipedia:Blastula" ] + } ], + "xrefs" : [ { + "val" : "BILA:0000059" + }, { + "val" : "BTO:0000128" + }, { + "val" : "GAID:1294" + }, { + "val" : "MESH:D036703" + }, { + "val" : "OGEM:000006" + }, { + "val" : "Wikipedia:Blastula" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007011" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", + "lbl" : "musculature of body", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", + "xrefs" : [ "VSAO:0000033" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "muscle system" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" - }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + "pred" : "hasExactSynonym", + "val" : "muscle system of body" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "hasExactSynonym", + "val" : "muscular system", + "xrefs" : [ "FMA:72954" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "pred" : "hasExactSynonym", + "val" : "musculature system", + "xrefs" : [ "BILA:0000088" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of all muscles", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of muscles of body", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate muscular system", + "xrefs" : [ "BTO:0001369" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "muskelsystem", + "xrefs" : [ "BTO:0001485" ] + } ], "xrefs" : [ { - "val" : "RO:0002180" + "val" : "AAO:0000307" + }, { + "val" : "BILA:0000088" + }, { + "val" : "BTO:0001369" + }, { + "val" : "BTO:0001485" + }, { + "val" : "EFO:0000801" + }, { + "val" : "FMA:72954" + }, { + "val" : "MA:0002888" + }, { + "val" : "MAT:0000025" + }, { + "val" : "MIAA:0000025" + }, { + "val" : "VSAO:0000033" + }, { + "val" : "XAO:0004042" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", + "lbl" : "organism substance", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "comments" : [ "TODO - add child relations from DOS" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "body fluid or substance", + "xrefs" : [ "MA:0002450" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "pred" : "hasExactSynonym", + "val" : "body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organism substance", + "xrefs" : [ "CARO:0000004" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance", + "xrefs" : [ "ZFA:0001487" ] + } ], "xrefs" : [ { - "val" : "RO:0002212" + "val" : "AAO:0010839" + }, { + "val" : "AEO:0000004" + }, { + "val" : "BILA:0000004" + }, { + "val" : "CALOHA:TS-2101" + }, { + "val" : "CARO:0000004" + }, { + "val" : "EHDAA2:0003004" + }, { + "val" : "EMAPA:35178" + }, { + "val" : "FBbt:00007019" + }, { + "val" : "FMA:9669" + }, { + "val" : "HAO:0000004" + }, { + "val" : "MA:0002450" + }, { + "val" : "NCIT:C13236" + }, { + "val" : "SPD:0000008" + }, { + "val" : "TAO:0001487" + }, { + "val" : "TGMA:0001824" + }, { + "val" : "VHOG:0001726" + }, { + "val" : "XAO:0004001" + }, { + "val" : "ZFA:0001487" + }, { + "val" : "galen:BodySubstance" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "negatively_regulates" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000464", + "lbl" : "anatomical space", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + "val" : "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "lumen" + }, { + "pred" : "hasBroadSynonym", + "val" : "space" + }, { + "pred" : "hasExactSynonym", + "val" : "lumen space" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "anatomical spaces", + "xrefs" : [ "ZFA:0001643" ] + } ], "xrefs" : [ { - "val" : "RO:0002213" + "val" : "AAO:0010110" + }, { + "val" : "AEO:0000005" + }, { + "val" : "BILA:0000005" + }, { + "val" : "CARO:0000005" + }, { + "val" : "EHDAA2:0003005" + }, { + "val" : "FBbt:00007017" + }, { + "val" : "FMA:5897" + }, { + "val" : "HAO:0000005" + }, { + "val" : "NCIT:C94478" + }, { + "val" : "TAO:0001668" + }, { + "val" : "TGMA:0001825" + }, { + "val" : "UMLS:C0524461" + }, { + "val" : "VHOG:0001728" + }, { + "val" : "XAO:0003190" + }, { + "val" : "ZFA:0001643" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "positively_regulates" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "lbl" : "material anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + "val" : "Anatomical entity that has mass.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002215" + "val" : "AAO:0010264" + }, { + "val" : "AEO:0000006" + }, { + "val" : "BILA:0000006" + }, { + "val" : "CARO:0000006" + }, { + "val" : "EHDAA2:0003006" + }, { + "val" : "FBbt:00007016" + }, { + "val" : "FMA:67165" + }, { + "val" : "HAO:0000006" + }, { + "val" : "TAO:0001836" + }, { + "val" : "TGMA:0001826" + }, { + "val" : "VHOG:0001721" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable of part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000466", + "lbl" : "immaterial anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + "val" : "Anatomical entity that has no mass.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "immaterial physical anatomical entity", + "xrefs" : [ "FMA:67112" ] + } ], "xrefs" : [ { - "val" : "RO:0002216" + "val" : "AAO:0010265" + }, { + "val" : "AEO:0000007" + }, { + "val" : "BILA:0000007" + }, { + "val" : "CARO:0000007" + }, { + "val" : "EHDAA2:0003007" + }, { + "val" : "FBbt:00007015" + }, { + "val" : "FMA:67112" + }, { + "val" : "HAO:0000007" + }, { + "val" : "TAO:0001835" + }, { + "val" : "TGMA:0001827" + }, { + "val" : "VHOG:0001727" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002219", - "lbl" : "surrounded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002220", - "lbl" : "adjacent to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000467", + "lbl" : "anatomical system", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x adjacent to y if and only if x and y share a boundary." + "val" : "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.", + "xrefs" : [ "CARO:0000011" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - 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"pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "AEO:0000011" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "adjacent_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002221", - "lbl" : "surrounds", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of surrounded by" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002223", - "lbl" : "starts", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of starts with" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002224", - "lbl" : "starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002224" + "val" : "BILA:0000011" + }, { + "val" : "BIRNLEX:14" + }, { + "val" : "BSA:0000049" + }, { + "val" : "CALOHA:TS-2088" + }, { + "val" : "CARO:0000011" + }, { + "val" : "EHDAA2:0003011" + }, { + "val" : "EHDAA:392" + }, { + "val" : "EMAPA:16103" + }, { + "val" : "EV:0100000" + }, { + "val" : "FBbt:00004856" + }, { + "val" : "FMA:7149" + }, { + "val" : "HAO:0000011" + }, { + "val" : "MA:0000003" + }, { + "val" : "NCIT:C12919" + }, { + "val" : "SCTID:278195005" + }, { + "val" : "TAO:0001439" + }, { + "val" : "TGMA:0001831" + }, { + "val" : "UMLS:C0460002" + }, { + "val" : "VHOG:0001725" + }, { + "val" : "WBbt:0005746" + }, { + "val" : "WBbt:0005763" + }, { + "val" : "Wikipedia:Organ_system" + }, { + "val" : "XAO:0003002" + }, { + "val" : "ZFA:0001439" + }, { + "val" : "galen:AnatomicalSystem" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts_with" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/EHDAA2_0001330" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002225", - "lbl" : "develops from part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002226", - "lbl" : "develops in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops_in y if x is located in y whilst x is developing" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", - "lbl" : "ends", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of ends with" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", - "lbl" : "ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000468", + "lbl" : "multicellular organism", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "Anatomical structure that is an individual member of a species and consists of more than one cell.", + "xrefs" : [ "CARO:0000012", "Wikipedia:Multi-cellular_organism", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "organism", + "xrefs" : [ "FBbt:00000001", "VHOG:0000671", "WBbt:0007833" ] + }, { + "pred" : "hasExactSynonym", + "val" : "multi-cellular organism", + "xrefs" : [ "CARO:0000012" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Koerper", + "xrefs" : [ "BTO:0001489" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103", "BIRNLEX:18", "FMA:256135", "NCIT:C13041" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole organism", + "xrefs" : [ "FBbt:00000001" ] + } ], "xrefs" : [ { - "val" : "RO:0002230" + "val" : "AAO:0010026" + }, { + "val" : "AEO:0000191" + }, { + "val" : "BILA:0000012" + }, { + "val" : "BIRNLEX:18" + }, { + "val" : "BSA:0000038" + }, { + "val" : "BTO:0000042" + }, { + "val" : "CARO:0000012" + }, { + "val" : "EFO:0002906" + }, { + "val" : "EHDAA2:0003103" + }, { + "val" : "EHDAA2:0003191" + }, { + "val" : "EHDAA:1" + }, { + "val" : "EMAPA:25765" + }, { + "val" : "EV:0100016" + }, { + "val" : "FBbt:00000001" + }, { + "val" : "FMA:256135" + }, { + "val" : "HAO:0000012" + }, { + "val" : "NCIT:C13041" + }, { + "val" : "SCTID:243928005" + }, { + "val" : "TADS:0000001" + }, { + "val" : "TAO:0001094" + }, { + "val" : "TGMA:0001832" + }, { + "val" : "VHOG:0000671" + }, { + "val" : "WBbt:0007833" + }, { + "val" : "Wikipedia:Multi-cellular_organism" + }, { + "val" : "XAO:0003004" + }, { + "val" : "ZFA:0001094" + }, { + "val" : "galen:Organism" + }, { + "val" : "ncithesaurus:Whole_Organism" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - split body and mc organism? body continues after death stage" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends_with" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002231", - "lbl" : "has start location", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000475", + "lbl" : "organism subdivision", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" + "val" : "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.", + "xrefs" : [ "CARO:0000032", "CARO:DOS", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomic region", + "xrefs" : [ "MA:0002433" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "body part" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body region", + "xrefs" : [ "FMA:7153" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardinal body part", + "xrefs" : [ "FMA:7153" ] + } ], "xrefs" : [ { - "val" : "RO:0002231" + "val" : "AAO:0010053" + }, { + "val" : "AEO:0000032" + }, { + "val" : "BILA:0000032" + }, { + "val" : "BIRNLEX:7" + }, { + "val" : "CALOHA:TS-2084" + }, { + "val" : "CARO:0000032" + }, { + "val" : "EFO:0000808" + }, { + "val" : "EHDAA2:0003032" + }, { + "val" : "EMAPA:36031" + }, { + "val" : "FBbt:00007009" + }, { + "val" : "FMA:7153" + }, { + "val" : "HAO:0000032" + }, { + "val" : "MA:0002433" + }, { + "val" : "MAT:0000293" + }, { + "val" : "MESH:D001829" + }, { + "val" : "MIAA:0000293" + }, { + "val" : "NCIT:C32221" + }, { + "val" : "TAO:0001308" + }, { + "val" : "TGMA:0001840" + }, { + "val" : "UMLS:C0229962" + }, { + "val" : "VHOG:0001758" + }, { + "val" : "Wikipedia:Body_part" + }, { + "val" : "XAO:0003013" + }, { + "val" : "ZFA:0001308" + }, { + "val" : "galen:BodyPart" } ], "basicPropertyValues" : [ { - 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"val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + "val" : "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "acellular anatomical structures", + "xrefs" : [ "ZFA:0000382" ] + } ], "xrefs" : [ { - "val" : "RO:0002232" + "val" : "AAO:0010268" + }, { + "val" : "AEO:0000040" + }, { + "val" : "BILA:0000040" + }, { + "val" : "CARO:0000040" + }, { + "val" : "EHDAA2:0003040" + }, { + "val" : "FBbt:00007013" + }, { + "val" : "FMA:63863" + }, { + "val" : "HAO:0000040" + }, { + "val" : "TAO:0000382" + }, { + "val" : "TGMA:0001841" + }, { + "val" : "XAO:0003162" + }, { + "val" : "ZFA:0000382" } ], "basicPropertyValues" : [ { - 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"subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002233" + "val" : "FBbt:00007277" + }, { + "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_input" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Has_input" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002234", - "lbl" : "has output", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000478", + "lbl" : "extraembryonic structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." + "val" : "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.", + "xrefs" : [ "CARO:DOS", "http://orcid.org/0000-0001-9114-8737", "https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002234" + "comments" : [ "see also conceptus extraembryonic component in EHDAA2." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "extra-embryonic structure" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "extraembryonic structures", + "xrefs" : [ "ZFA:0000020" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "extraembryonic tissue" } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "xrefs" : [ { + "val" : "AAO:0010020" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_output" + "val" : "AEO:0000042" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Has_output" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002252", - "lbl" : "connecting branch of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." - }, + "val" : "BILA:0000042" + }, { + "val" : "CALOHA:TS-2119" + }, { + "val" : "CARO:0000042" + }, { + "val" : "EHDAA2:0003042" + }, { + "val" : "EHDAA:46" + }, { + "val" : "FBbt:00005835" + }, { + "val" : "FMA:85537" + }, { + "val" : "HAO:0000042" + }, { + "val" : "NCIT:C34055" + }, { + "val" : "SCTID:314908006" + }, { + "val" : "TAO:0000020" + }, { + "val" : "TGMA:0001843" + }, { + "val" : "UMLS:C1282438" + }, { + "val" : "VHOG:0000292" + }, { + "val" : "XAO:0004005" + }, { + "val" : "ZFA:0000020" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2212" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002253", - "lbl" : "has connecting branch", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", + "lbl" : "tissue", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of connecting branch of" + "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", + "xrefs" : [ "CARO:0000043" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002254", - "lbl" : "has developmental contribution from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002255", - "lbl" : "developmentally contributes to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of has developmental contribution from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002256", - "lbl" : "developmentally induced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002257", - "lbl" : "developmentally induces", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Inverse of developmentally induced by" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002258", - "lbl" : "developmentally preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" - }, - "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "false" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002263", - "lbl" : "acts upstream of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002264", - "lbl" : "acts upstream of or within", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "affects" + "pred" : "hasExactSynonym", + "val" : "portion of tissue", + "xrefs" : [ "CARO:0000043" ] + }, { + "pred" : "hasExactSynonym", + "val" : "tissue portion" + }, { + "pred" : "hasNarrowSynonym", + "val" : "simple tissue", + "xrefs" : [ "AEO:0000043" ] } ], - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002285", - "lbl" : "developmentally replaces", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. 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We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002286", - "lbl" : "developmentally succeeded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Inverse of developmentally preceded by" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002287", - "lbl" : "part of developmental precursor of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002292", - "lbl" : "expresses", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002295", - "lbl" : "results in developmental progression of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." - }, "xrefs" : [ { - "val" : "RO:0002295" + "val" : "AAO:0000607" + }, { + "val" : "AAO:0010054" + }, { + "val" : "AEO:0000043" + }, { + "val" : "BILA:0000043" + }, { + "val" : "BIRNLEX:19" + }, { + "val" : "CALOHA:TS-2090" + }, { + "val" : "CARO:0000043" + }, { + "val" : "EHDAA2:0003043" + }, { + "val" : "EMAPA:35868" + }, { + "val" : "FBbt:00007003" + }, { + "val" : "FMA:9637" + }, { + "val" : "HAO:0000043" + }, { + "val" : "MA:0003002" + }, { + "val" : "MESH:D014024" + }, { + "val" : "NCIT:C12801" + }, { + "val" : "TAO:0001477" + }, { + "val" : "TGMA:0001844" + }, { + "val" : "UMLS:C0040300" + }, { + "val" : "VHOG:0001757" + }, { + "val" : "WBbt:0005729" + }, { + "val" : "XAO:0003040" + }, { + "val" : "ZFA:0001477" + }, { + "val" : "galen:Tissue" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. 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Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].", + "xrefs" : [ "FMA:FMA", "Wikipedia:Stratified_epithelium", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "stratified epithelium" + }, { + "pred" : "hasRelatedSynonym", + "val" : "laminated epithelium", + "xrefs" : [ "BTO:0002074" ] + } ], "xrefs" : [ { - "val" : "RO:0002299" + "val" : "AAO:0010059" + }, { + "val" : "AEO:0000069" + }, { + "val" : "BILA:0000069" + }, { + "val" : "BTO:0002074" + }, { + "val" : "CARO:0000069" + }, { + "val" : "EHDAA2:0003069" + }, { + "val" : "FMA:45562" + }, { + "val" : "HAO:0000069" + }, { + "val" : "NCIT:C33622" + }, { + "val" : "SCTID:309044005" + }, { + "val" : "TAO:0001494" + }, { + "val" : "UMLS:C0682575" + }, { + "val" : "Wikipedia:Stratified_epithelium" + }, { + "val" : "XAO:0004006" + }, { + "val" : "ZFA:0001494" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_maturation_of" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002304", - "lbl" : "causally upstream of, positive effect", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000490", + "lbl" : "unilaminar epithelium", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." + "val" : "Epithelium which consists of a single layer of epithelial cells. 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"val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", - "lbl" : "tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002371", + "lbl" : "bone marrow", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The soft tissue that fills the cavities of bones.", + "xrefs" : [ "MGI:cwg", "MP:0002397" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "anatomical tube" + "val" : "medulla ossea", + "xrefs" : [ "BTO:0000141", "FMA:9608" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "medulla ossium", + "xrefs" : [ "BTO:0000141", "Wikipedia:Bone_marrow" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "duct" - } ], - "xrefs" : [ { - "val" : "galen:Tube" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000043", - "lbl" : "tendon", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Dense regular connective tissue that connects muscle to bone[VSAO].", - "xrefs" : [ "GO_REF:0000034", "VSAO:0000073", "Wikipedia:Tendon", "http://dx.plos.org/10.1371/journal.pone.0051070" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { "pred" : "hasRelatedSynonym", - 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See also: Leydig and epigonal organs" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider placement of NCIT:C53466 medullary bone" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000058", - "lbl" : "duct", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", + "lbl" : "connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A tubular structure that transports secreted or excreted substances.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165", "http://www.siumed.edu/~dking2/intro/glands.htm#ducts" ] + "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] }, - 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In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "pred" : "hasExactSynonym", - "val" : "biological structure" + "val" : "muscular tissue" }, { "pred" : "hasExactSynonym", - "val" : "connected biological structure", - "xrefs" : [ "CARO:0000003" ] + "val" : "portion of muscle tissue", + "xrefs" : [ "FMA:9641" ] + }, { + "pred" : "hasExactSynonym", + "val" : "textus muscularis" } ], "xrefs" : [ { - "val" : "AAO:0010825" - }, { - "val" : "AEO:0000003" - }, { - "val" : "BILA:0000003" - }, { - "val" : "CARO:0000003" - }, { - "val" : "EHDAA2:0003003" - }, { - "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" - }, { - "val" : "FMA:305751" + "val" : "AAO:0000306" }, { - "val" : "FMA:67135" + "val" : "AEO:0000122" }, { - "val" : "GAID:781" + "val" : "CALOHA:TS-0642" }, { - "val" : "HAO:0000003" + "val" : "EHDAA2:0003122" }, { - "val" : "MA:0003000" + "val" : "EMAPA:32715" }, { - 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See https://github.com/obophenotype/uberon/issues/77" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004120", + "lbl" : "mesoderm-derived structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - 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This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000467", - "lbl" : "anatomical system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", + "lbl" : "gastrula", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.", - "xrefs" : [ "CARO:0000011" ] + "val" : "Organism at the gastrula stage.", + "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "system", - "xrefs" : [ "GO:0048731" ] - }, { - "pred" : "hasExactSynonym", - "val" : "body system", - "xrefs" : [ "BIRNLEX:14" ] - }, { - "pred" : "hasExactSynonym", - "val" : "connected anatomical system", - "xrefs" : [ "CARO:0000011" ] - }, { "pred" : "hasExactSynonym", - "val" : "organ system" + "val" : "gastrula embryo", + "xrefs" : [ "BILA:0000060" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "anatomical systems", - "xrefs" : [ "ZFA:0001439" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000007" - }, { - "val" : "AEO:0000011" + "val" : "blastocystis trilaminaris", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "BILA:0000011" + "pred" : "hasRelatedSynonym", + "val" : "tri-laminar disc", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "BIRNLEX:14" + "pred" : "hasRelatedSynonym", + "val" : "tri-laminar disk", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "BSA:0000049" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "CALOHA:TS-2088" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "CARO:0000011" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disc", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "EHDAA2:0003011" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "EHDAA:392" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILA:0000060" }, { - "val" : "EMAPA:16103" + "val" : "BTO:0001403" }, { - "val" : "EV:0100000" + "val" : "FBbt:00005317" }, { - "val" : "FBbt:00004856" + "val" : "FMA:293108" }, { - "val" : "FMA:7149" + "val" : "GAID:1302" }, { - "val" : "HAO:0000011" + "val" : "MESH:D005775" }, { - "val" : "MA:0000003" + "val" : "MIAA:0000179" }, { - "val" : "NCIT:C12919" + "val" : "NCIT:C34057" }, { - "val" : "SCTID:278195005" + "val" : "NCIT:C34058" }, { - "val" : "TAO:0001439" + "val" : "UMLS:C0017199" }, { - "val" : "TGMA:0001831" + "val" : "UMLS:C1284022" }, { - "val" : "UMLS:C0460002" + "val" : "Wikipedia:Gastrula" }, { - "val" : "VHOG:0001725" + "val" : "Wikipedia:Trilaminar_blastocyst" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007012" }, { - "val" : "WBbt:0005746" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004755", + "lbl" : "skeletal tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000015", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/134" ] + }, + "comments" : [ "Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from" ], + "xrefs" : [ { + "val" : "EMAPA:37744" }, { - "val" : "WBbt:0005763" + "val" : "MA:0003047" }, { - "val" : "Wikipedia:Organ_system" + "val" : "SCTID:309311006" }, { - "val" : "XAO:0003002" + "val" : "VSAO:0000015" }, { - "val" : "ZFA:0001439" + "val" : "XAO:0004038" }, { - "val" : "galen:AnatomicalSystem" + "val" : "ZFA:0005619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", + "lbl" : "skeletal element", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "AAO:0011129" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "val" : "TAO:0001890" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "VSAO:0000128" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "XAO:0004012" + }, { + "val" : "ZFA:0005494" }, { + "val" : "galen:SkeletalStructure" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/EHDAA2_0001330" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "lbl" : "multicellular organism", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", + "lbl" : "articular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that is an individual member of a species and consists of more than one cell.", - "xrefs" : [ "CARO:0000012", "Wikipedia:Multi-cellular_organism", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Anatomical system that consists of all the joints of the body.", + "xrefs" : [ "VSAO:0000181" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "organism", - "xrefs" : [ "FBbt:00000001", "VHOG:0000671", "WBbt:0007833" ] - }, { "pred" : "hasExactSynonym", - "val" : "multi-cellular organism", - "xrefs" : [ "CARO:0000012" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Koerper", - "xrefs" : [ "BTO:0001489" ] + "val" : "joint system", + "xrefs" : [ "FMA:23878" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "body", - "xrefs" : [ "AEO:0000103", "BIRNLEX:18", "FMA:256135", "NCIT:C13041" ] + "pred" : "hasExactSynonym", + "val" : "set of all joints of body", + "xrefs" : [ "FMA:23878" ] }, { "pred" : "hasRelatedSynonym", - "val" : "whole body", - "xrefs" : [ "BTO:0001489" ] + "val" : "set of all joints" }, { "pred" : "hasRelatedSynonym", - "val" : "whole organism", - "xrefs" : [ "FBbt:00000001" ] + "val" : "set of joints of body", + "xrefs" : [ "FMA:23878" ] } ], "xrefs" : [ { - "val" : "AAO:0010026" - }, { - "val" : "AEO:0000191" - }, { - "val" : "BILA:0000012" - }, { - "val" : "BIRNLEX:18" - }, { - "val" : "BSA:0000038" - }, { - "val" : "BTO:0000042" - }, { - "val" : "CARO:0000012" - }, { - "val" : "EFO:0002906" - }, { - "val" : "EHDAA2:0003103" - }, { - "val" : "EHDAA2:0003191" - }, { - "val" : "EHDAA:1" - }, { - "val" : "EMAPA:25765" - }, { - "val" : "EV:0100016" + "val" : "EMAPA:35150" }, { - "val" : "FBbt:00000001" + "val" : "FMA:23878" }, { - "val" : "FMA:256135" + "val" : "MA:0003007" }, { - "val" : "HAO:0000012" + "val" : "SCTID:361827000" }, { - "val" : "NCIT:C13041" + "val" : "VSAO:0000181" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", + "lbl" : "chordamesoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The central region of trunk mesoderm. 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"xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "One of the two elevated edges of the neural groove[GO,MP].", + "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "acellular anatomical structures", - "xrefs" : [ "ZFA:0000382" ] + "pred" : "hasExactSynonym", + "val" : "medullary fold", + "xrefs" : [ "MP:0011256" ] } ], "xrefs" : [ { - "val" : "AAO:0010268" - }, { - "val" : "AEO:0000040" - }, { - "val" : "BILA:0000040" - }, { - "val" : "CARO:0000040" - }, { - "val" : "EHDAA2:0003040" + "val" : "EHDAA2:0001249" }, { - "val" : "FBbt:00007013" + "val" : "FMA:295618" }, { - "val" : "FMA:63863" + "val" : "NCIT:C34223" }, { - "val" : "HAO:0000040" + "val" : "SCTID:361461009" }, { - "val" : "TAO:0000382" + "val" : "UMLS:C0814993" }, { - "val" : "TGMA:0001841" + "val" : "Wikipedia:Neural_fold" }, { - "val" : "XAO:0003162" + "val" : "XAO:0004087" }, { - "val" : "ZFA:0000382" + "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", - "lbl" : "anatomical cluster", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005068", + "lbl" : "neural rod", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical group whose component anatomical structures lie in close proximity to each other.", - "xrefs" : [ "FBbt:00007277" ] + "val" : "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].", + "xrefs" : [ "GO:0014024", "ZFA:0000133" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "neural tube rod", + "xrefs" : [ "GO:0014027" ] + } ], "xrefs" : [ { - "val" : "FBbt:00007277" + "val" : "EFO:0003498" }, { - "val" : "VHOG:0001737" + "val" : "TAO:0000133" + }, { + "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000478", - "lbl" : "extraembryonic structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", + "lbl" : "muscle structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.", - "xrefs" : [ "CARO:DOS", "http://orcid.org/0000-0001-9114-8737", "https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279" ] + "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", + "xrefs" : [ "GO:0061061" ] }, - "comments" : [ "see also conceptus extraembryonic component in EHDAA2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "extra-embryonic structure" + "val" : "musculus", + "xrefs" : [ "FMA:30316" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "extraembryonic structures", - "xrefs" : [ "ZFA:0000020" ] + "val" : "muscle" }, { "pred" : "hasRelatedSynonym", - "val" : "extraembryonic tissue" + "val" : "muscle element" } ], "xrefs" : [ { - "val" : "AAO:0010020" - }, { - "val" : "AEO:0000042" - }, { - "val" : "BILA:0000042" - }, { - "val" : "CALOHA:TS-2119" - }, { - "val" : "CARO:0000042" - }, { - "val" : "EHDAA2:0003042" - }, { - "val" : "EHDAA:46" - }, { - "val" : "FBbt:00005835" - }, { - "val" : "FMA:85537" - }, { - "val" : "HAO:0000042" - }, { - "val" : "NCIT:C34055" - }, { - "val" : "SCTID:314908006" + "val" : "FMA:30316" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", + "lbl" : "epithelial fold", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelial sheet bent on a linear axis.", + "xrefs" : [ "GO:0060571" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005256", + "lbl" : "trunk mesenchyme", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mesenchyme that is part of a developing trunk.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "trunk and cervical mesenchyme", + "xrefs" : [ "EHDAA2:0002092" ] + } ], + "xrefs" : [ { + "val" : "EFO:0003485" }, { - "val" : "TAO:0000020" + "val" : "EHDAA2:0002092" }, { - "val" : "TGMA:0001843" + "val" : "EHDAA:377" }, { - "val" : "UMLS:C1282438" + "val" : "EMAPA:16177" }, { - "val" : "VHOG:0000292" + "val" : "TAO:0000081" }, { - "val" : "XAO:0004005" + "val" : "VHOG:0000281" }, { - "val" : "ZFA:0000020" + "val" : "ZFA:0000081" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18409,78 +20403,83 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", - "lbl" : "tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005291", + "lbl" : "embryonic tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", - "xrefs" : [ "CARO:0000043" ] + "val" : "A portion of tissue that is part of an embryo.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "portion of tissue", - "xrefs" : [ "CARO:0000043" ] + "val" : "portion of embryonic tissue", + "xrefs" : [ "OBOL:automatic" ] }, { + "pred" : "hasRelatedSynonym", + "val" : "developing tissue" + } ], + "xrefs" : [ { + "val" : "CALOHA:TS-2100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005388", + "lbl" : "photoreceptor array", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An array of photoreceptors and any supporting cells found in an eye.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "tissue portion" - }, { - "pred" : "hasNarrowSynonym", - "val" : "simple tissue", - "xrefs" : [ "AEO:0000043" ] + "val" : "light-sensitive tissue" } ], "xrefs" : [ { - "val" : "AAO:0000607" - }, { - "val" : "AAO:0010054" - }, { - "val" : "AEO:0000043" - }, { - "val" : "BILA:0000043" - }, { - "val" : "BIRNLEX:19" - }, { - "val" : "CALOHA:TS-2090" - }, { - "val" : "CARO:0000043" - }, { - "val" : "EHDAA2:0003043" - }, { - "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" - }, { - "val" : "FMA:9637" - }, { - "val" : "HAO:0000043" - }, { - "val" : "MA:0003002" - }, { - "val" : "MESH:D014024" - }, { - "val" : "NCIT:C12801" - }, { - "val" : "TAO:0001477" + "val" : "FBbt:00004200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005423", + "lbl" : "developing anatomical structure", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "developing structure" }, { - "val" : "TGMA:0001844" + "pred" : "hasRelatedSynonym", + "val" : "developmental structure" }, { - "val" : "UMLS:C0040300" + "pred" : "hasRelatedSynonym", + "val" : "developmental tissue", + "xrefs" : [ "MIAA:0000019" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000125" }, { - "val" : "VHOG:0001757" + "val" : "CALOHA:TS-2122" }, { - "val" : "WBbt:0005729" + "val" : "EHDAA2:0003125" }, { - "val" : "XAO:0003040" + "val" : "FBbt:00007006" }, { - "val" : "ZFA:0001477" + "val" : "FMA:292313" }, { - "val" : "galen:Tissue" + "val" : "MIAA:0000019" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "changed label and definition to reflect CARO2" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -18495,45 +20494,17 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000481", - "lbl" : "multi-tissue structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005764", + "lbl" : "acellular membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.", - "xrefs" : [ "CARO:0000055", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "An acellular anatomical structure that is the bounding layer of a anatomical structure.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "multi-tissue structures", - "xrefs" : [ "ZFA:0001488" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { - "val" : "AAO:0010048" - }, { - "val" : "AEO:0000055" - }, { - "val" : "BILA:0000055" - }, { - "val" : "CARO:0000055" - }, { - "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" - }, { - "val" : "HAO:0000055" - }, { - "val" : "TAO:0001488" - }, { - "val" : "TGMA:0001847" - }, { - "val" : "VHOG:0001762" - }, { - "val" : "XAO:0003037" - }, { - "val" : "ZFA:0001488" + "val" : "FMA:63871" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -18550,127 +20521,138 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "lbl" : "epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "lbl" : "basement membrane of epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].", - "xrefs" : [ "Wikipedia:Epithelium", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.", + "xrefs" : [ "Wikipedia:Basement_membrane", "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "epithelial tissue" + "val" : "basement membrane of connective tissue", + "xrefs" : [ "FMA:63872" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "portion of epithelium", - "xrefs" : [ "FMA:9639" ] + "val" : "membrana basalis", + "xrefs" : [ "Wikipedia:Basement_membrane" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "basement membrane", + "xrefs" : [ "FMA:63872" ] } ], "xrefs" : [ { - "val" : "AAO:0000144" - }, { - "val" : "AAO:0010055" - }, { - "val" : "AEO:0000066" - }, { - "val" : "BILA:0000066" - }, { - "val" : "BTO:0000416" - }, { - "val" : "CALOHA:TS-0288" - }, { - "val" : "CARO:0000066" - }, { - "val" : "EHDAA2:0003066" - }, { - "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" - }, { - "val" : "FMA:9639" + "val" : "AAO:0010596" }, { - "val" : "GAID:402" + "val" : "FMA:63872" }, { - "val" : "HAO:0000066" + "val" : "GAID:915" }, { - "val" : "MA:0003060" + "val" : "NCIT:C13191" }, { - "val" : "MESH:D004848" + "val" : "SCTID:68989006" }, { - "val" : "NCIT:C12710" + "val" : "UMLS:C0004799" }, { - "val" : "SCTID:31610004" + "val" : "Wikipedia:Basement_membrane" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { - "val" : "TAO:0001486" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", + "lbl" : "notochordal plate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", + "xrefs" : [ "VHOG:0001212" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], + "xrefs" : [ { + "val" : "EHDAA2:0001278" }, { - "val" : "UMLS:C0014609" + "val" : "EHDAA:264" }, { - "val" : "VHOG:0000387" + "val" : "EMAPA:16101" }, { - "val" : "Wikipedia:Epithelium" + "val" : "NCIT:C34231" }, { - "val" : "XAO:0003045" + "val" : "UMLS:C1518429" }, { - "val" : "ZFA:0001486" + "val" : "VHOG:0001212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ordering; awaiting confirmation from JB" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000486", - "lbl" : "multilaminar epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", + "lbl" : "notochordal process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].", - "xrefs" : [ "FMA:FMA", "Wikipedia:Stratified_epithelium", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", + "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "stratified epithelium" + "pred" : "hasRelatedSynonym", + "val" : "chordamesoderm" }, { "pred" : "hasRelatedSynonym", - "val" : "laminated epithelium", - "xrefs" : [ "BTO:0002074" ] + "val" : "presumptive notochord" } ], "xrefs" : [ { - "val" : "AAO:0010059" - }, { - "val" : "AEO:0000069" - }, { - "val" : "BILA:0000069" - }, { - "val" : "BTO:0002074" - }, { - "val" : "CARO:0000069" - }, { - "val" : "EHDAA2:0003069" + "val" : "EHDAA2:0001279" }, { - "val" : "FMA:45562" + "val" : "EHDAA:224" }, { - "val" : "HAO:0000069" + "val" : "EMAPA:16102" }, { - "val" : "NCIT:C33622" + "val" : "FMA:293135" }, { - "val" : "SCTID:309044005" + "val" : "NCIT:C34232" }, { - "val" : "TAO:0001494" + "val" : "UMLS:C1518430" }, { - "val" : "UMLS:C0682575" + "val" : "VHOG:0001213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006595", + "lbl" : "presumptive endoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Presumptive structure of the blastula that will develop into endoderm.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "AAO:0000471" }, { - "val" : "Wikipedia:Stratified_epithelium" + "val" : "EFO:0003437" }, { - "val" : "XAO:0004006" + "val" : "TAO:0000416" }, { - "val" : "ZFA:0001494" + "val" : "ZFA:0000416" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18678,212 +20660,207 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000490", - "lbl" : "unilaminar epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006598", + "lbl" : "presumptive structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].", - "xrefs" : [ "FMA:45561", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Portion of embryonic tissue determined by fate mapping to become a structure.", + "xrefs" : [ "GOC:CVS", "GOC:YMB", "ZFA:0001116" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "simple epithelium", - "xrefs" : [ "FMA:45561" ] + "val" : "future structure" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "unilaminar epithelia", - "xrefs" : [ "ZFA:0001495" ] + "pred" : "hasExactSynonym", + "val" : "presumptive structures", + "xrefs" : [ "ZFA:0001116" ] } ], "xrefs" : [ { - "val" : "AAO:0010062" - }, { - "val" : "AEO:0000073" - }, { - "val" : "BILA:0000073" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000073" - }, { - "val" : "EHDAA2:0003073" - }, { - "val" : "FMA:45561" - }, { - "val" : "HAO:0000073" - }, { - "val" : "NCIT:C33554" - }, { - "val" : "SCTID:309043004" - }, { - "val" : "TAO:0001495" - }, { - "val" : "UMLS:C0682574" + "val" : "AAO:0000479" }, { - "val" : "XAO:0004007" + "val" : "TAO:0001116" }, { - "val" : "ZFA:0001495" + "val" : "ZFA:0001116" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" + "val" : "Consider merging with anlage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000922", - "lbl" : "embryo", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006601", + "lbl" : "presumptive ectoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", - "xrefs" : [ "BTO:0000379", "FB:FBrf0039741", "FB:FBrf0041814", "GO:0009790", "Wikipedia:Embryo" ] + "val" : "Presumptive structure of the blastula that will develop into ectoderm.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic organism", - "xrefs" : [ "BILA:0000056" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing organism", - "xrefs" : [ "BILA:0000056" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "developmental tissue" + "val" : "presumptive epidermis", + "xrefs" : [ "ZFA:0001376" ] } ], "xrefs" : [ { - "val" : "AAO:0011035" - }, { - "val" : "AEO:0000169" - }, { - "val" : "BILA:0000056" - }, { - "val" : "BSA:0000039" - }, { - "val" : "BTO:0000379" + "val" : "AAO:0000470" }, { - "val" : "CALOHA:TS-0229" + "val" : "EFO:0003466" }, { - "val" : "EFO:0001367" + "val" : "TAO:0001376" }, { - "val" : "EHDAA2:0000002" + "val" : "XAO:0004132" }, { - "val" : "EHDAA2_RETIRED:0003236" + "val" : "ZFA:0001376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006603", + "lbl" : "presumptive mesoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Presumptive structure of the blastula that will develop into mesoderm.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "AAO:0000476" }, { - "val" : "EHDAA:38" + "val" : "EFO:0003467" }, { - "val" : "EMAPA:16039" + "val" : "TAO:0001377" }, { - "val" : "FBbt:00000052" + "val" : "ZFA:0001377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006984", + "lbl" : "anatomical surface", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] + }, + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "BILA:0000010" }, { - "val" : "FMA:69068" + "val" : "CARO:0001002" }, { - "val" : "GAID:963" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "MAT:0000226" + "val" : "FMA:24137" }, { - "val" : "MESH:D004622" + "val" : "NCIT:C34022" }, { - "val" : "MIAA:0000019" + "val" : "UMLS:C1515977" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", + "lbl" : "cleaving embryo", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Organism at the cleavage stage.", + "xrefs" : [ "OBOL:automatic" ] + }, + "xrefs" : [ { + "val" : "BILA:0000058" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", + "lbl" : "presumptive gut", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "future digestive tract" }, { - "val" : "NCIT:C28147" + "pred" : "hasExactSynonym", + "val" : "future digestive tube" }, { - "val" : "OGEM:000001" + "pred" : "hasExactSynonym", + "val" : "future gut" }, { - "val" : "SCTID:57991002" + "pred" : "hasExactSynonym", + "val" : "primitive gut" }, { - "val" : "UMLS:C0013935" + "pred" : "hasRelatedSynonym", + "val" : "embryonic digestive tube" }, { - "val" : "VHOG:0001766" + "pred" : "hasRelatedSynonym", + "val" : "primordial digestive tube" }, { - "val" : "Wikipedia:Embryo" + "pred" : "hasRelatedSynonym", + "val" : "primordial gut" + } ], + "xrefs" : [ { + "val" : "BILA:0000084" }, { - "val" : "XAO:0000113" + "val" : "NCIT:C34268" }, { - "val" : "ZFA:0000103" + "val" : "SCTID:360394002" }, { - "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" + "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/503" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "lbl" : "germ layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007100", + "lbl" : "primary circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.", - "xrefs" : [ "Wikipedia:Germ_layer", "https://github.com/obophenotype/uberon/issues/203" ] + "val" : "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].", + "xrefs" : [ "GO:0007507" ] }, - "comments" : [ "Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "Gene notes: Bmp, Nkx, Gata" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "embryonic tissue", - "xrefs" : [ "FMA:69069" ] - }, { - "pred" : "hasExactSynonym", - "val" : "germinal layer", - "xrefs" : [ "ncithesaurus:Germinal_Layer" ] - }, { "pred" : "hasNarrowSynonym", - "val" : "primary germ layer", - "xrefs" : [ "GO:0001704", "ZFA:0001122" ] + "val" : "dorsal tube", + "xrefs" : [ "Wikipedia:Heart" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layer" + "pred" : "hasNarrowSynonym", + "val" : "heart", + "xrefs" : [ "GO:0007507" ] }, { "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layers" + "val" : "adult heart", + "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "AAO:0000480" - }, { - "val" : "BILA:0000035" - }, { - "val" : "BTO:0000556" - }, { - "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" - }, { - "val" : "FMA:69069" - }, { - "val" : "GAID:1303" - }, { - "val" : "MESH:D005855" - }, { - "val" : "NCIT:C12950" - }, { - "val" : "NCIT:C54105" - }, { - "val" : "TAO:0001122" - }, { - "val" : "UMLS:C0920502" - }, { - "val" : "UMLS:C1708239" - }, { - "val" : "VHOG:0001223" - }, { - "val" : "Wikipedia:Germ_layer" - }, { - "val" : "XAO:0003011" + "val" : "TADS:0000147" }, { - "val" : "ZFA:0001122" + "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18891,371 +20868,276 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", - "lbl" : "ectoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007135", + "lbl" : "neural keel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", - "xrefs" : [ "Wikipedia:Ectoderm" ] + "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.", + "xrefs" : [ "ZFIN:ZDB-PUB-961014-576" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic ectoderm", - "xrefs" : [ "VHOG:0000153" ] + "pred" : "hasRelatedSynonym", + "val" : "presumptive central nervous system", + "xrefs" : [ "ZFA:0000131" ] } ], "xrefs" : [ { - "val" : "AAO:0000137" - }, { - "val" : "BILA:0000036" - }, { - "val" : "BTO:0000315" - }, { - "val" : "CALOHA:TS-0216" - }, { - 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"val" : "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.", - "xrefs" : [ "Wikipedia:Endoderm" ] + "val" : "A presumptive structure that has the potential to develop into a presomitic mesoderm.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "entoderm", - "xrefs" : [ "DOI:10.5962/bhl.title.1013" ] + "val" : "presumptive segmental plates", + "xrefs" : [ "ZFA:0000053" ] } ], "xrefs" : [ { - "val" : "AAO:0000139" - }, { - "val" : "BILA:0000038" - 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"val" : "VHOG:0000154" + "pred" : "hasExactSynonym", + "val" : "future paraxial mesoderm" + } ], + "xrefs" : [ { + "val" : "EFO:0003443" }, { - "val" : "Wikipedia:Endoderm" + "val" : "TAO:0000591" }, { - "val" : "XAO:0000090" + "val" : "XAO:0004134" }, { - "val" : "ZFA:0000017" + "val" : "ZFA:0000591" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "lbl" : "mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007503", + "lbl" : "epithelial vesicle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The middle germ layer of the embryo, between the endoderm and ectoderm.", - "xrefs" : [ "Wikipedia:Mesoderm" ] + "val" : "A closed epithelium with a lumen.", + "xrefs" : [ "AEO:JB" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "embryonic mesoderm", - "xrefs" : [ "VHOG:0000152" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "entire mesoderm", - "xrefs" : [ "SCTID:362854004", "https://orcid.org/0000-0002-6601-2165" ] + "xrefs" : [ { + "val" : "AEO:0000119" }, { - "pred" : "hasRelatedSynonym", - "val" : "mesodermal mantle" + "val" : "EHDAA2:0003119" } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007524", + "lbl" : "dense mesenchyme tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mesenchyme with little extracellular matrix.", + "xrefs" : [ "AEO:JB" ] + }, "xrefs" : [ { - "val" : "AAO:0000304" - }, { - "val" : "BILA:0000037" - }, { - "val" : "BTO:0000839" - }, { - "val" : "CALOHA:TS-0623" - }, { - "val" : "EFO:0001981" - }, { - "val" : "EHDAA2:0001128" - }, { - "val" : "EHDAA:124" - }, { - "val" : "EHDAA:160" - }, { - "val" : "EHDAA:183" - }, { - "val" : "EMAPA:16083" - }, { - "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" - }, { - "val" : "FMA:69072" - }, { - "val" : "GAID:522" - }, { - "val" : "MAT:0000174" - }, { - "val" : "MESH:D008648" - }, { - "val" : "MIAA:0000174" - }, { - "val" : "NCIT:C12750" - }, { - "val" : "SCTID:362854004" - }, { - "val" : "TAO:0000041" - }, { - "val" : "UMLS:C0025485" - }, { - "val" : "VHOG:0000152" - }, { - "val" : "Wikipedia:Mesoderm" - }, { - "val" : "XAO:0000050" + "val" : "AEO:0000146" }, { - "val" : "ZFA:0000041" + "val" : "EHDAA2:0003146" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007845", + "lbl" : "regular connective tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.", + "xrefs" : [ "FMA:20103" ] + }, + "xrefs" : [ { + "val" : "FMA:20103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "lbl" : "stomodeum", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007846", + "lbl" : "dense regular connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.", - "xrefs" : [ "Wikipedia:Stomodeum", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/326" ] + "val" : "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000050", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "stomodeal-hypophyseal primordium", - "xrefs" : [ "XAO:0000269" ] - }, { "pred" : "hasExactSynonym", - "val" : "mouth primordium", - "xrefs" : [ "XAO:0000269" ] + "val" : "dense fibrous connective tissue", + "xrefs" : [ "FMA:64781" ] }, { "pred" : "hasExactSynonym", - "val" : "primitive oral cavity", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "dense regular collagenous connective tissue", + "xrefs" : [ "FMA:64781" ] }, { "pred" : "hasExactSynonym", - "val" : "stomatodeum", - "xrefs" : [ "Wikipedia:Stomodeum" ] + "val" : "dense regular collagenous tissue", + "xrefs" : [ "FMA:64781" ] }, { "pred" : "hasExactSynonym", - "val" : "stomodaeum" - }, { - "pred" : "hasRelatedSynonym", - "val" : "mouth pit", - "xrefs" : [ "EMAPA:16263" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "oral ectoderm", - "xrefs" : [ "ZFA:0001290", "ZFIN:ZDB-PUB-100726-23" ] + "val" : "regular dense connective tissue" }, { - "pred" : "hasRelatedSynonym", - "val" : "oral pit", - "xrefs" : [ "EMAPA:16263" ] + "pred" : "hasExactSynonym", + "val" : "typus regularis (textus connectivus collagenosus compactus)", + "xrefs" : [ "FMA:64781" ] } ], "xrefs" : [ { - "val" : "BTO:0004224" - }, { - "val" : "EHDAA2:0001929" - }, { - "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" + "val" : "FMA:64781" }, { - "val" : "FMA:295846" + "val" : "NCIT:C33453" }, { - "val" : "NCIT:C34306" + "val" : "SCTID:22560007" }, { - "val" : "TAO:0001290" + "val" : "UMLS:C0225333" }, { - "val" : "TGMA:0000135" + "val" : "VSAO:0000050" }, { - "val" : "UMLS:C1514977" + "val" : "Wikipedia:Dense_regular_connective_tissue" }, { - "val" : "Wikipedia:Stomodeum" + "val" : "XAO:0004030" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", + "lbl" : "entire embryonic mesenchyme", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Sum total of mesenchyme in the embryo.", + "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] + }, + "xrefs" : [ { + "val" : "EHDAA2:0001113" }, { - "val" : "XAO:0000269" + "val" : "EHDAA:177" }, { - "val" : "ZFA:0001290" + "val" : "EMAPA:16097" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" + "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000949", - "lbl" : "endocrine system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", + "lbl" : "trunk paraxial mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.", - "xrefs" : [ "NLM:endocrine+system", "Wikipedia:Endocrine_system" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "endocrine glandular system", - "xrefs" : [ "EHDAA2:0002224" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocrine system" + "val" : "trunk and cervical paraxial mesenchyme", + "xrefs" : [ "EHDAA2:0002094" ] }, { - "pred" : "hasExactSynonym", - "val" : "systema endocrinum" + "pred" : "hasRelatedSynonym", + "val" : "trunk paraxial mesenchyme", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] } ], "xrefs" : [ { - "val" : "AAO:0010279" - }, { - "val" : "CALOHA:TS-1301" - }, { - "val" : "EFO:0002969" - }, { - "val" : "EHDAA2:0002224" - }, { - "val" : "EMAPA:35306" - }, { - "val" : "EV:0100128" - }, { - "val" : "FBbt:00005068" - }, { - "val" : "FMA:9668" - }, { - "val" : "GAID:439" - }, { - "val" : "MA:0000012" - }, { - "val" : "MESH:D004703" - }, { - "val" : "NCIT:C12705" - }, { - "val" : "SCTID:278876000" - }, { - "val" : "TAO:0001158" - }, { - "val" : "UMLS:C0014136" - }, { - "val" : "VHOG:0000098" - }, { - "val" : "Wikipedia:Endocrine_system" - }, { - "val" : "XAO:0000158" - }, { - "val" : "ZFA:0001158" + "val" : "EHDAA2:0002094" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -19263,126 +21145,52 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000970", - "lbl" : "eye", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organ that detects light.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "light-detecting organ" - }, { - "pred" : "hasRelatedSynonym", - "val" : "visual apparatus", - "xrefs" : [ "EV:0100336" ] + "pred" : "hasExactSynonym", + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { - "val" : "BILA:0000017" - }, { - "val" : "BTO:0000439" - }, { - "val" : "CALOHA:TS-0309" - }, { - "val" : "EFO:0000827" - }, { - "val" : "EV:0100336" - }, { - "val" : "FBbt:00005162" - }, { - "val" : "GAID:69" - }, { - "val" : "MAT:0000140" - }, { - "val" : "MESH:D005123" - }, { - "val" : "MIAA:0000140" + "val" : "CARO:0010000" }, { - "val" : "Wikipedia:Eye" + "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000982", - "lbl" : "skeletal joint", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010199", + "lbl" : "bona-fide anatomical boundary", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].", - "xrefs" : [ "GO_REF:0000034", "VSAO:0000101", "Wikipedia:Joint", "http://dx.plos.org/10.1371/journal.pone.0051070" ] + "val" : "An anatomical boundary that corresponds to some physical discontinuity.", + "xrefs" : [ "CARO:0001004" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "articulation", - "xrefs" : [ "VSAO:0000101" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "joint", - "xrefs" : [ "FMA:7490", "VSAO:0000101" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "articular joint", - "xrefs" : [ "BTO:0001686" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "joints", - "xrefs" : [ "ZFA:0001596" ] - } ], + "comments" : [ "One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. 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however, most visceral muscles in arthropods are actually striated." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "skeleton system" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasNarrowSynonym", - "val" : "set of all bones and joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Skelettsystem", - "xrefs" : [ "BTO:0001486" ] + "val" : "visceral muscle" } ], - "xrefs" : [ { - "val" : "AAO:0000566" - }, { - "val" : "BTO:0001486" - }, { - "val" : "CALOHA:TS-1320" - }, { - "val" : "EFO:0000806" - }, { - "val" : "EHDAA2:0003168" - }, { - "val" : "EMAPA:35773" - }, { - "val" : "FMA:23881" - }, { - "val" : "MA:0000018" - }, { - "val" : "NCIT:C12788" - }, { - "val" : "TAO:0000434" - }, { - "val" : "UMLS:C0037253" - }, { - "val" : "VHOG:0001254" - }, { - "val" : "VSAO:0000027" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" }, { - "val" : "XAO:0003060" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-16T10:17:46Z" }, { - "val" : "ZFA:0000434" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001474", - "lbl" : "bone element", + "id" : "http://purl.obolibrary.org/obo/UBERON_8600006", + "lbl" : "visceral striated muscle tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Skeletal element that is composed of bone tissue.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000057", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/277" ] + "val" : "A striated muscle tissue that is associated with soft internal organs (viscera).", + "xrefs" : [ "PMID:8720463", "https://pressbooks.pub/rbtallitsch/chapter/chapter-6-muscle-tissue/" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "bone organ", - "xrefs" : [ "FMA:5018" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "bone", - "xrefs" : [ "AEO:0000082", "BTO:0000140", "MA:0001459", "VHOG:0001190" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "bones", - "xrefs" : [ "ZFA:0001514" ] + "val" : "striated visceral muscle tissue" } ], - "xrefs" : [ { - "val" : "AAO:0000047" - }, { - "val" : "AEO:0000082" - }, { - "val" : "BTO:0000140" - }, { - "val" : "CALOHA:TS-0088" - }, { - "val" : "EFO:0000298" - }, { - "val" : "EHDAA2:0003082" - }, { - "val" : "EMAPA:32782" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" }, { - "val" : "ENVO:00002039" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-16T10:34:43Z" }, { - "val" : "EV:0100140" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { - "val" : "FMA:30317" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "FMA:5018" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "val" : "GAID:92" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "MA:0001459" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "MAT:0000299" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "MIAA:0000299" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "val" : "NCIT:C12366" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "val" : "SCTID:90780006" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" }, { - "val" : "TAO:0001514" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { - "val" : "UMLS:C0262950" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "VHOG:0001190" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "val" : "VSAO:0000057" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "Wikipedia:Bone" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "XAO:0000169" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { - "val" : "ZFA:0001514" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "galen:Bone" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "lbl" : "digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A tube extending from the mouth to the anus.", - "xrefs" : [ "Wikipedia:Talk:Human_gastrointestinal_tract", "https://github.com/geneontology/go-ontology/issues/7549" ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "gut" - }, { - "pred" : "hasExactSynonym", - "val" : "digestive tube" - }, { - "pred" : "hasExactSynonym", - "val" : "enteric tract", - "xrefs" : [ "ZFA:0000112" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary canal" - }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "digestive canal", - "xrefs" : [ "BTO:0000058" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut tube" - } ], + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0010023" - }, { - "val" : "BILA:0000083" - }, { - "val" : "BTO:0000511" - }, { - "val" : "BTO:0000545" - }, { - "val" : "EHDAA2:0000726" - }, { - "val" : "EHDAA:518" - }, { - "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" - }, { - "val" : "FMA:45615" - }, { - "val" : "MA:0000917" - }, { - "val" : "NCIT:C34082" - }, { - "val" : "TAO:0000112" + "val" : "BFO:0000066" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "TGMA:0001819" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" }, { - "val" : "UMLS:C0017189" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "xrefs" : [ { + "val" : "GOREL:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "VHOG:0000309" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "xrefs" : [ { + "val" : "GOREL:0002004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "WBbt:0005743" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { - "val" : "ZFA:0000112" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "galen:AlimentaryTract" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_41324" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001630", - "lbl" : "muscle organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].", - "xrefs" : [ "GO:0007517" ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "muscle", - "xrefs" : [ "ZFA:0005145" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37474" - }, { - "val" : "EV:0100146" - }, { - "val" : "FMA:5022" - }, { - "val" : "GAID:131" - }, { - "val" : "MA:0000015" - }, { - "val" : "SCTID:71616004" - }, { - "val" : "TAO:0005145" - }, { - "val" : "VHOG:0001245" - }, { - "val" : "XAO:0000172" - }, { - "val" : "ZFA:0005145" - }, { - "val" : "galen:Muscle" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002036", - "lbl" : "striated muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle tissue that contains fibers that are divided by transverse bands into striations.", - "xrefs" : [ "CL:0000737", "GOC:dph", "GOC:mtg_muscle" ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "striated muscle" - } ], - "xrefs" : [ { - "val" : "AAO:0010762" - }, { - "val" : "AEO:0000140" - }, { - "val" : "CALOHA:TS-2047" - }, { - "val" : "EHDAA2:0003140" - }, { - "val" : "EMAPA:36390" - }, { - "val" : "FMA:67905" - }, { - "val" : "MA:0002438" - }, { - "val" : "NCIT:C12436" - }, { - "val" : "UMLS:C1331262" - }, { - "val" : "WBbt:0005779" - }, { - "val" : "Wikipedia:Striated_muscle" - }, { - "val" : "galen:StriatedMuscle" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002050", - "lbl" : "embryonic structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that is part of an embryo.", - "xrefs" : [ "BTO:0000174", "ZFIN:curator" ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "developing embryonic structure", - "xrefs" : [ "FBbt:00004208" ] - }, { - "pred" : "hasExactSynonym", - "val" : "embryonic anatomical structure", - "xrefs" : [ "RETIRED_EHDAA2:0003169" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonale Struktur", - "xrefs" : [ "BTO:0000174" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "embryonic structures", - "xrefs" : [ "ZFA:0001105" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000138" - }, { - "val" : "BILA:0000034" - }, { - "val" : "BTO:0000174" - }, { - "val" : "CALOHA:TS-2110" - }, { - "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" - }, { - "val" : "FMA:69067" - }, { - "val" : "GAID:407" - }, { - "val" : "MESH:D004628" - }, { - "val" : "NCIT:C13229" - }, { - "val" : "RETIRED_EHDAA2:0003169" - }, { - "val" : "SCTID:667009" - }, { - "val" : "TAO:0001105" - }, { - "val" : "UMLS:C0013948" - }, { - "val" : "VSAO:0000178" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "val" : "XAO:0003042" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "ZFA:0001105" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", - "lbl" : "trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. 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" }, - "comments" : [ "Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "NC", - "xrefs" : [ "XAO:0000048" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "crista neuralis", - "xrefs" : [ "Wikipedia:Neural_crest" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neural crest material", - "xrefs" : [ "VHOG:0000057" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010578" - }, { - "val" : "BTO:0001764" - }, { - "val" : "CALOHA:TS-0676" - }, { - "val" : "EHDAA2:0004419" - }, { - "val" : "EMAPA:32737" - }, { - "val" : "FMA:86666" - }, { - "val" : "GAID:1310" - }, { - "val" : "MAT:0000066" - }, { - "val" : "MESH:D009432" - }, { - "val" : "MIAA:0000066" - }, { - "val" : "NCIT:C34222" - }, { - "val" : "SCTID:361462002" - }, { - "val" : "UMLS:C0027789" - }, { - "val" : "VHOG:0000057" - }, { - "val" : "Wikipedia:Neural_crest" - }, { - "val" : "XAO:0000048" - }, { - "val" : "ZFA:0000045" - }, { - "val" : "neuronames:1366" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002346", - "lbl" : "neurectoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002113", + "lbl" : "has presynaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Embryonic ectoderm that gives rise to nervous tissue.", - "xrefs" : [ "Wikipedia:Neuroectoderm" ] + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural ectoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "neuroectoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epithelium tubi neuralis; neuroectoderma", - "xrefs" : [ "Wikipedia:Neuroectoderm" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neuaral ectoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral neurogenic region", - "xrefs" : [ "VHOG:0000150" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011074" - }, { - "val" : "BILA:0000039" - }, { - "val" : "CALOHA:TS-1212" - }, { - "val" : "EHDAA2:0001248" - }, { - "val" : "EHDAA:1498" - }, { - "val" : "EHDAA:255" - }, { - "val" : "EMAPA:16073" - }, { - "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" - }, { - "val" : "FMA:87657" - }, { - "val" : "MAT:0000176" - }, { - "val" : "MIAA:0000176" - }, { - "val" : "NCIT:C34228" - }, { - "val" : "TAO:0001120" - }, { - "val" : "UMLS:C1518271" - }, { - "val" : "VHOG:0000150" - }, { - "val" : "Wikipedia:Neuroectoderm" - }, { - "val" : "XAO:0000042" - }, { - "val" : "ZFA:0001120" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002365", - "lbl" : "exocrine gland", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas.", - "xrefs" : [ "Wikipedia:Exocrine_gland" ] + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ducted gland", - "xrefs" : [ "AEO:0000097" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "glandula exocrina", - "xrefs" : [ "Wikipedia:Exocrine_gland" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000097" - }, { - "val" : "BTO:0000765" - }, { - "val" : "CALOHA:TS-2012" - }, { - "val" : "EHDAA2:0003097" - }, { - "val" : "EMAPA:35327" - }, { - "val" : "FMA:9596" - }, { - "val" : "GAID:34" - }, { - "val" : "MA:0002564" - }, { - "val" : "MESH:D005088" - }, { - "val" : "NCIT:C12712" - }, { - "val" : "SCTID:115976003" - }, { - "val" : "UMLS:C0015282" - }, { - "val" : "Wikipedia:Exocrine_gland" - } ], + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002368", - "lbl" : "endocrine gland", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].", - "xrefs" : [ "Wikipedia:Endocrine_gland" ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - 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See also: Leydig and epigonal organs" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider placement of NCIT:C53466 medullary bone" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "lbl" : "connective tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue", - "xrefs" : [ "FMA:9640" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bindegewebe", - "xrefs" : [ "BTO:0000421" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000098" - }, { - "val" : "BTO:0000421" - }, { - "val" : "CALOHA:TS-2009" - }, { - "val" : "EFO:0000952" - }, { - "val" : "EMAPA:35251" - }, { - "val" : "FMA:9640" - }, { - "val" : "GAID:100" - }, { - "val" : "MA:0000011" - }, { - "val" : "MAT:0000301" - }, { - "val" : "MESH:D003238" - }, { - "val" : "MIAA:0000301" - }, { - "val" : "NCIT:C12374" - }, { - "val" : "SCTID:361919005" - }, { - "val" : "TAO:0001641" - }, { - "val" : "UMLS:C0009780" - }, { - "val" : "VSAO:0000017" - }, { - "val" : "XAO:0001017" - }, { - "val" : "ZFA:0001632" - }, { - "val" : "galen:ConnectiveTissue" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "lbl" : "muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", - "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." }, - "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus muscularis" - } ], - "xrefs" : [ { - "val" : "AAO:0000306" - }, { - "val" : "AEO:0000122" - }, { - "val" : "CALOHA:TS-0642" - }, { - "val" : "EHDAA2:0003122" - }, { - "val" : "EMAPA:32715" - }, { - "val" : "FMA:9641" - }, { - "val" : "MA:0002437" - }, { - "val" : "MESH:D009132" - }, { - "val" : "NCIT:C12435" - }, { - "val" : "SCTID:91727004" - }, { - "val" : "UMLS:C2328219" - }, { - "val" : "Wikipedia:Muscle_tissue" - }, { - "val" : "galen:MuscleTissue" - } ], + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "haematological system" - }, { - "pred" : "hasExactSynonym", - "val" : "haemopoietic system" - }, { - "pred" : "hasExactSynonym", - "val" : "organa haemopoietica" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Blutbildungssystem", - "xrefs" : [ "BTO:0000570" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "haematopoietic system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematological system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematolymphoid system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hemopoietic system" - } ], - "xrefs" : [ { - "val" : "AAO:0011002" - }, { - "val" : "BTO:0000570" - }, { - "val" : "CALOHA:TS-0449" - }, { - "val" : "EFO:0000798" - }, { - "val" : "EMAPA:35402" - }, { - "val" : "EV:0100045" - }, { - "val" : "FMA:9667" - }, { - "val" : "GAID:1008" - }, { - "val" : "MA:0002434" - }, { - "val" : "MAT:0000022" - }, { - "val" : "MESH:D006413" - }, { - "val" : "MIAA:0000022" - }, { - "val" : "NCIT:C12909" - }, { - "val" : "SCTID:362587009" - }, { - "val" : "TAO:0005023" - }, { - "val" : "UMLS:C0018957" - }, { - "val" : "VHOG:0001624" - }, { - "val" : "Wikipedia:Haematopoiesis" + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. 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" }, { - "val" : "XAO:0000122" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { - "val" : "ZFA:0005023" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002405", - "lbl" : "immune system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.", - "xrefs" : [ "Wikipedia:Immune_system" ] + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "xrefs" : [ { - "val" : "AAO:0011003" - }, { - "val" : "BILA:0000104" - }, { - "val" : "BTO:0005810" - }, { - "val" : "FMA:9825" - }, { - "val" : "GAID:328" - }, { - "val" : "MA:0002711" - }, { - "val" : "MESH:D007107" - }, { - "val" : "NCIT:C12735" - }, { - "val" : "SCTID:362590003" - }, { - "val" : "TAO:0001159" - }, { - "val" : "UMLS:C0020962" - }, { - "val" : "VHOG:0001247" - }, { - "val" : "Wikipedia:Immune_system" - }, { - "val" : "XAO:0003152" - }, { - "val" : "ZFA:0001159" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "lbl" : "bone tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). 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For example, in the realm of anatomy this should hold between an artery and an anatomical structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002530", - "lbl" : "gland", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that functions as a secretory or excretory organ.", - "xrefs" : [ "MGI:csmith", "MP:0002163" ] + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "glandular organ", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Druese", - "xrefs" : [ "BTO:0000522" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "glandula", - "xrefs" : [ "BTO:0000522", "Wikipedia:Gland" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000212" - }, { - "val" : "AEO:0000096" - }, { - "val" : "BTO:0000522" - }, { - "val" : "EFO:0000797" - }, { - "val" : "EHDAA2:0003096" - }, { - "val" : "EHDAA:2161" - }, { - "val" : "EMAPA:18425" - }, { - "val" : "FBbt:00100317" - }, { - "val" : "FMA:7146" - }, { - "val" : "FMA:86294" - }, { - "val" : "HAO:0000375" - }, { - "val" : "MA:0003038" - }, { - "val" : "MAT:0000021" - }, { - "val" : "MIAA:0000021" - }, { - "val" : "NCIT:C13319" - }, { - "val" : "SCTID:134358001" - }, { - "val" : "UMLS:C1285092" - }, { - "val" : "Wikipedia:Gland" - }, { - "val" : "WikipediaCategory:Glands" - }, { - "val" : "galen:Gland" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. 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In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] + "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" - } ], - "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" - }, { - "val" : "NCIT:C34007" - }, { - "val" : "galen:Cavity" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segmental plate" - }, { - "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] - } ], + "val" : "has developmental precursor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" - }, { - "val" : "XAO:0000057" - }, { - "val" : "ZFA:0000279" + "val" : "RO:0002211" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", - "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ventral lateral plate mesoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "blood islands" - }, { - "pred" : "hasRelatedSynonym", - "val" : "VBI" - }, { - "pred" : "hasRelatedSynonym", - "val" : "caudal hematopoietic tissue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior ICM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior blood island" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral blood island" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011006" - }, { - "val" : "EFO:0003489" - }, { - "val" : "EHDAA:207" - }, { - "val" : "NCIT:C34113" - }, { - "val" : "TAO:0000094" - }, { - "val" : "TE:E5.11.2.0.0.0.4" - }, { - "val" : "UMLS:C1511224" - }, { - "val" : "VHOG:0000085" - }, { - "val" : "Wikipedia:Blood_island_of_umbilical_vesicle" - }, { - "val" : "XAO:0000067" - }, { - "val" : "ZFA:0000094" + "val" : "RO:0002212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "lbl" : "axial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.", - "xrefs" : [ "GO:0048318", "Wikipedia:Chordamesoderm" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm", - "xrefs" : [ "Wikipedia:Chordamesoderm" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011017" - }, { - "val" : "EFO:0003647" - }, { - "val" : "TAO:0001204" - }, { - "val" : "VHOG:0000107" - }, { - "val" : "Wikipedia:Chordamesoderm" - }, { - "val" : "XAO:0000205" - }, { - "val" : "ZFA:0001204" + "val" : "RO:0002213" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "lbl" : "neural plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].", - "xrefs" : [ "ISBN:0815318960", "OMD:neural+plate", "Wikipedia:Neural_plate", "ZFIN:curator" ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina neuralis", - "xrefs" : [ "Wikipedia:Neural_plate" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011072" - }, { - "val" : "BTO:0001765" - }, { - "val" : "DHBA:10153" - }, { - "val" : "DMBA:15565" - }, { - "val" : "EHDAA:346" - }, { - "val" : "EHDAA:902" - }, { - "val" : "EMAPA:35593" - }, { - "val" : "FMA:293879" - }, { - "val" : "NCIT:C34225" - }, { - "val" : "RETIRED_EHDAA2:0001252" - }, { - "val" : "TAO:0000132" - }, { - "val" : "UMLS:C0920623" - }, { - "val" : "VHOG:0000068" - }, { - "val" : "Wikipedia:Neural_plate" - }, { - "val" : "XAO:0000249" - }, { - "val" : "ZFA:0000132" - }, { - "val" : "neuronames:1362" + "val" : "RO:0002215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "lbl" : "paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].", - "xrefs" : [ "GO:0048339", "https://github.com/obophenotype/uberon/issues/30" ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "paraxial mesenchyme", - "xrefs" : [ "ZFA:0000255", "https://github.com/obophenotype/uberon/issues/30", "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "somitic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesoderma paraxiale", - "xrefs" : [ "Wikipedia:Paraxial_mesoderm" ] - } ], "xrefs" : [ { - "val" : "AAO:0010568" - }, { - "val" : "EFO:0003515" - }, { - "val" : "EMAPA:16183" - }, { - "val" : "EMAPA:16751" - }, { - "val" : "FMA:293145" - }, { - "val" : "NCIT:C34244" - }, { - "val" : "SCTID:361475002" - }, { - "val" : "TAO:0000255" - }, { - "val" : "UMLS:C1284009" - }, { - "val" : "VHOG:0000114" - }, { - "val" : "Wikipedia:Paraxial_mesoderm" - }, { - "val" : "XAO:0000259" - }, { - "val" : "ZFA:0000255" + "val" : "RO:0002216" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "lbl" : "lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].", - "xrefs" : [ "MP:0010117", "Wikipedia:Lateral_plate_mesoderm" ] + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "LPM", - "xrefs" : [ "ZFA:0000121" ] - }, { - "pred" : "hasExactSynonym", - "val" : "lateral mesoderm", - "xrefs" : [ "GO:0048368" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "lateral plate" - }, { - "pred" : "hasRelatedSynonym", - "val" : "lateral plate mesenchyme", - "xrefs" : [ "EHDAA2:0000919" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesoderma laminae lateralis", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0010574" - }, { - "val" : "EHDAA2:0000919" - }, { - "val" : "EHDAA:379" - }, { - "val" : "EMAPA:16179" - }, { - "val" : "FMA:293149" - }, { - "val" : "NCIT:C34199" - }, { - "val" : "SCTID:361477005" - }, { - "val" : "TAO:0000121" - }, { - "val" : "UMLS:C1517749" - }, { - "val" : "VHOG:0000118" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm" - }, { - "val" : "XAO:0000311" - }, { - "val" : "ZFA:0000121" + "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003082", - "lbl" : "myotome", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.", - "xrefs" : [ "AEO:0001018" ] + "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - 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Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0010015" - }, { - "val" : "AEO:0000024" - }, { - "val" : "BILA:0000024" - }, { - "val" : "CARO:0000024" - }, { - "val" : "EHDAA2:0003024" - }, { - "val" : "HAO:0000024" - }, { - "val" : "TADS:0000598" - }, { - "val" : "TAO:0000496" - }, { - "val" : "TGMA:0001837" - }, { - "val" : "VHOG:0001723" - }, { - "val" : "XAO:0003041" - }, { - "val" : "ZFA:0000496" + "val" : "RO:0002230" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "lbl" : "mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. 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TODO - add spatial relationships to halves of LPM. 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It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - 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"val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004290", - "lbl" : "dermomyotome", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The bilaminar epithelium formed from the myotome and dermatome.", - "xrefs" : [ "AEO:0000214" ] + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "dermamyotome", - "xrefs" : [ "VHOG:0000676" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "dermomyotomes", - "xrefs" : [ "VHOG:0000676" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010572" - }, { - "val" : "AEO:0000214" - }, { - "val" : "EHDAA2:0003259" - }, { - "val" : "EMAPA:31109" - }, { - "val" : "FMA:295654" - }, { - "val" : "NCIT:C34140" - }, { - "val" : "TAO:0001513" - }, { - "val" : "UMLS:C1511786" - }, { - "val" : "VHOG:0000676" - }, { - "val" : "ZFA:0001513" + "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004456", - "lbl" : "entire sense organ system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Sum of all sensory systems in an organism.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sense organ system", - "xrefs" : [ "FMA:78499" ] - } ], - "xrefs" : [ { - "val" : "FMA:78499" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004716", - "lbl" : "conceptus", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].", - "xrefs" : [ "BTO:0003834", "Wikipedia:Conceptus" ] + "val" : "Inverse of developmentally preceded by" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryo plus adnexa" - } ], "xrefs" : [ { - "val" : "AEO:0000194" - }, { - "val" : "BTO:0003834" - }, { - "val" : "EHDAA2:0000001" - }, { - "val" : "EHDAA2:0003235" - }, { - "val" : "EMAPA:36040" - }, { - "val" : "NCIT:C34131" - }, { - "val" : "UMLS:C1516779" - }, { - "val" : "Wikipedia:Conceptus" + "val" : "RO:0002295" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", - "lbl" : "gastrula", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the gastrula stage.", - "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gastrula embryo", - "xrefs" : [ "BILA:0000060" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocystis trilaminaris", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastocyst", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar germ", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BILA:0000060" - }, { - "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" - }, { - "val" : "FMA:293108" - }, { - "val" : "GAID:1302" - }, { - "val" : "MESH:D005775" - }, { - "val" : "MIAA:0000179" - }, { - "val" : "NCIT:C34057" - }, { - "val" : "NCIT:C34058" - }, { - "val" : "UMLS:C0017199" - }, { - "val" : "UMLS:C1284022" - }, { - "val" : "Wikipedia:Gastrula" - }, { - "val" : "Wikipedia:Trilaminar_blastocyst" + "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004755", - "lbl" : "skeletal tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of anatomical entity", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000015", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/134" ] - }, - "comments" : [ "Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:37744" - }, { - "val" : "MA:0003047" - }, { - "val" : "SCTID:309311006" - }, { - "val" : "VSAO:0000015" - }, { - "val" : "XAO:0004038" - }, { - "val" : "ZFA:0005619" + "val" : "RO:0002297" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", - "lbl" : "skeletal element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" - }, { - "val" : "galen:SkeletalStructure" + "val" : "RO:0002298" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" - }, { - "val" : "MA:0003007" - }, { - "val" : "SCTID:361827000" - }, { - "val" : "VSAO:0000181" + "val" : "RO:0002299" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - 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"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "FBbt:00005811" + "val" : "RO:0002305" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - 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If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "presumptive epidermis", - "xrefs" : [ "ZFA:0001376" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000470" - }, { - "val" : "EFO:0003466" - }, { - "val" : "TAO:0001376" - }, { - "val" : "XAO:0004132" - }, { - "val" : "ZFA:0001376" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "lbl" : "presumptive mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Presumptive structure of the blastula that will develop into mesoderm.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "xrefs" : [ { - "val" : "AAO:0000476" - }, { - "val" : "EFO:0003467" - }, { - "val" : "TAO:0001377" - }, { - "val" : "ZFA:0001377" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006984", - "lbl" : "anatomical surface", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", - "xrefs" : [ "CARO:0001002" ] + "val" : "inverse of upstream of" }, - "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "BILA:0000010" - }, { - "val" : "CARO:0001002" - }, { - "val" : "EHDAA2_RETIRED:0003192" - }, { - "val" : "FMA:24137" - }, { - "val" : "NCIT:C34022" - }, { - "val" : "UMLS:C1515977" + "val" : "RO:0002404" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", - "lbl" : "cleaving embryo", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the cleavage stage.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "xrefs" : [ { - "val" : "BILA:0000058" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", - "lbl" : "presumptive gut", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future digestive tract" - }, { - "pred" : "hasExactSynonym", - "val" : "future digestive tube" - }, { - "pred" : "hasExactSynonym", - "val" : "future gut" - }, { - "pred" : "hasExactSynonym", - "val" : "primitive gut" - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic digestive tube" - }, { - "pred" : "hasRelatedSynonym", - "val" : "primordial digestive tube" - }, { - "pred" : "hasRelatedSynonym", - "val" : "primordial gut" - } ], + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BILA:0000084" - }, { - "val" : "NCIT:C34268" - }, { - "val" : "SCTID:360394002" - }, { - "val" : "UMLS:C1514442" + "val" : "RO:0002411" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007100", - "lbl" : "primary circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].", - "xrefs" : [ "GO:0007507" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "comments" : [ "Gene notes: Bmp, Nkx, Gata" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "dorsal tube", - "xrefs" : [ "Wikipedia:Heart" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "heart", - "xrefs" : [ "GO:0007507" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "adult heart", - "xrefs" : [ "FBbt:00003154" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "TADS:0000147" - }, { - "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007135", - "lbl" : "neural keel", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; 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Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "prospective neuroectoderm", - "xrefs" : [ "ZFA:0000063" ] - }, { - "pred" : "hasExactSynonym", - "val" : "prospective vegetal ectoderm", - "xrefs" : [ "ZFA:0000063" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003424" - }, { - "val" : "TAO:0000063" - }, { - "val" : "ZFA:0000063" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007285", - "lbl" : "presumptive paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. 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Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. 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Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. 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Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. 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See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "definition" : { + "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "add to RO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034769", - "lbl" : "lymphomyeloid tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", + "lbl" : "layer part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "FMA:79770" - }, { - "val" : "NCIT:C41168" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", + "lbl" : "posteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] + "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], - "xrefs" : [ { - "val" : "CARO:0020001" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", + "lbl" : "protects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", + "lbl" : "proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034969", - "lbl" : "epithelial layer of duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", + "lbl" : "sexually_homologous_to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "duct epithelium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ductal epithelium" - } ], - "xrefs" : [ { - "val" : "NCIT:C25787" - }, { - "val" : "UMLS:C1512086" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", + "lbl" : "site_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], - "xrefs" : [ { - "val" : "FMA:293105" + "pred" : "hasRelatedSynonym", + "val" : "capable_of_has_part" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24822,411 +25530,916 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", - "lbl" : "visceral muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", + "lbl" : "subdivision of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] - }, - "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral muscle" - } ], + "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:17:46Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600006", - "lbl" : "visceral striated muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A striated muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "PMID:8720463", "https://pressbooks.pub/rbtallitsch/chapter/chapter-6-muscle-tissue/" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "striated visceral muscle tissue" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:34:43Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", - "lbl" : "blood_and_immune_upper_slim", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", + "lbl" : "transitively distally connected to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-03-31T09:17:34Z" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", - "lbl" : "eye_upper_slim", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", + "lbl" : "transitively proximally connected to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "comments" : [ "a subset of general classes related to specific cell types in the eye." ] + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", - "lbl" : "general_cell_types_upper_slim", + "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", + "lbl" : "trunk_part_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "comments" : [ "a subset of general classes of cell types in the cell ontology." ] + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", - "lbl" : "kidney_upper_slim", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { - "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-11-22T11:18:57Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", - "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", - "lbl" : "latin term", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", - "lbl" : "plural term", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", - "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "xrefs" : [ { + "val" : "IAO:0000233" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, + "xrefs" : [ { + "val" : "IAO:0000700" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." + "val" : "A synonym type for describing abbreviations or initalisms" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "A synonym type for describing pluralization synonyms" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/RO_0002259", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", + "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], + "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-31T09:17:34Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", + "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", + "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", + "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-11-22T11:18:57Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", + "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", + "lbl" : "latin term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", + "lbl" : "plural term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", + "lbl" : "a mis-spelling that is in common use and thus recorded", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -25242,11 +26455,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -25263,6 +26478,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -25278,11 +26494,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -25298,23 +26516,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -25324,6 +26571,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -27117,6 +28376,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0001667", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0016477" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001677", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0022618" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001677", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006413" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001677", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_0044207" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0001704", "pred" : "is_a", @@ -27523,6 +28794,58 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006310", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0006259" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009059" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0019538" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0010467" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0006414" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/RO_0002224", + "obj" : "http://purl.obolibrary.org/obo/GO_0006413" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/RO_0002230", + "obj" : "http://purl.obolibrary.org/obo/GO_0006415" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006413", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006413", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006413", + "pred" : "http://purl.obolibrary.org/obo/RO_0002224", + "obj" : "http://purl.obolibrary.org/obo/GO_0001677" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006414", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009059" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006414", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006415", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032984" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006415", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006810", "pred" : "is_a", @@ -27735,10 +29058,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044249" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009059", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_1901576" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -27967,6 +29286,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0019226", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0007268" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0019538", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044238" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0019538", + "pred" : "http://purl.obolibrary.org/obo/RO_0004007", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0019724", "pred" : "is_a", @@ -28003,6 +29330,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0021915", "pred" : "http://purl.obolibrary.org/obo/RO_0002296", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022411", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022411", + "pred" : "http://purl.obolibrary.org/obo/RO_0002590", + "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0022414", "pred" : "is_a", @@ -28015,6 +29350,38 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0022600", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0007586" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022607", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022607", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0044085" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022607", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_0005575" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022613", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044085" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0065003" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0071826" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0022613" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_1990904" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0023052", "pred" : "is_a", @@ -28247,6 +29614,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0032940", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0140352" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0032984", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0022411" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0032984", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0043933" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0032984", + "pred" : "http://purl.obolibrary.org/obo/RO_0002590", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", "pred" : "is_a", @@ -28483,6 +29862,26 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043292", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0043933", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0043933", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044085", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0071840" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044207", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_1990904" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044207", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0005737" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044237", "pred" : "is_a", @@ -28491,6 +29890,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044237", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044238", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044249", "pred" : "is_a", @@ -28947,6 +30350,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0062023", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0065003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0022607" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0065003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0043933" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0065003", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0065007", "pred" : "is_a", @@ -28972,9 +30387,13 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099503" }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0071704", + "sub" : "http://purl.obolibrary.org/obo/GO_0071826", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" + "obj" : "http://purl.obolibrary.org/obo/GO_0043933" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0071826", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_1990904" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0071840", "pred" : "is_a", @@ -29259,14 +30678,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140546", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0098542" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1902105", "pred" : "is_a", @@ -29299,6 +30710,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_1903706", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", "obj" : "http://purl.obolibrary.org/obo/GO_0030097" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_1990904", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" }, { "sub" : "http://purl.obolibrary.org/obo/GO_2000026", "pred" : "is_a", @@ -29611,6 +31026,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070046", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0070045" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -29839,6 +31266,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000050216", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000001006" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000020", "pred" : "is_a", @@ -33752,6 +35183,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000006", @@ -34666,6 +36101,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002371" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001677", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0044207" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001704", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], @@ -34897,6 +36339,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000034" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019538", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", + "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019724", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0002376" ], @@ -34911,6 +36360,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001049" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022411", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005575" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022600", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003008" ], @@ -34918,6 +36374,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007586" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022607", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005575" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022618", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_1990904" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0023061", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032940" ], @@ -35023,6 +36493,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032984", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022411" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035148", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], @@ -35093,6 +36570,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043933", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045321", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0001775" ], @@ -35303,6 +36787,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0065003", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0070013", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031974" ], @@ -35317,6 +36808,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0099500" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0071826", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_1990904" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0072175", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0035148" ], @@ -36115,6 +37613,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/src/ontology/subsets/general_cell_types_upper_slim.obo b/src/ontology/subsets/general_cell_types_upper_slim.obo index ff7dddd78..ce6d8abd7 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.obo +++ b/src/ontology/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -121,7 +126,7 @@ name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell @@ -132,7 +137,7 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] @@ -146,7 +151,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -171,7 +176,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -213,7 +218,7 @@ def: "A cell that is within the developmental lineage of gametes and is able to comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim subset: ubprop:upper_level -xref: ZFA:0009016 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: capable_of GO:0022414 ! reproductive process @@ -228,7 +233,7 @@ synonym: "colony forming unit monocyte" RELATED [] synonym: "monocyte stem cell" RELATED [] xref: CALOHA:TS-1195 xref: FMA:83553 -xref: ZFA:0009017 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -252,7 +257,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -275,7 +280,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell @@ -297,7 +302,7 @@ synonym: "early lymphocyte progenitor" RELATED [] synonym: "ELP" RELATED OMO:0003000 [] synonym: "lymphoid stem cell" RELATED [] synonym: "lymphopoietic stem cell" RELATED [] -xref: ZFA:0009023 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009023 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell @@ -312,7 +317,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -332,10 +337,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -351,7 +356,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -367,14 +372,14 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -383,7 +388,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -395,7 +400,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -418,7 +423,7 @@ xref: CALOHA:TS-1001 xref: FMA:62870 xref: MESH:D013601 xref: VHOG:0001479 -xref: ZFA:0009046 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009046 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000542 {is_inferred="true"} ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity @@ -438,7 +443,7 @@ xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 xref: MESH:D010010 -xref: ZFA:0009047 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell @@ -475,7 +480,7 @@ xref: BTO:0000539 xref: BTO:0001026 xref: CALOHA:TS-0422 xref: FMA:62854 -xref: ZFA:0009048 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte @@ -513,10 +518,10 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "motoneuron" EXACT [] xref: BTO:0000312 -xref: FBbt:00005123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83617 xref: WBbt:0005409 -xref: ZFA:0009052 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000527 ! efferent neuron property_value: RO:0002175 NCBITaxon:9606 @@ -526,11 +531,11 @@ name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] subset: human_reference_atlas xref: BTO:0001037 -xref: FBbt:00005124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 xref: MESH:D011984 xref: WBbt:0005759 -xref: ZFA:0009053 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009053 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000526 ! afferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception @@ -544,7 +549,7 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 -xref: ZFA:0009064 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) @@ -563,9 +568,9 @@ synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: CALOHA:TS-0415 -xref: FBbt:00005144 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 -xref: ZFA:0009073 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 @@ -574,7 +579,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -598,7 +603,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -615,7 +620,7 @@ synonym: "fat cell" EXACT [] xref: BTO:0000443 xref: CALOHA:TS-0012 xref: FMA:63880 -xref: ZFA:0009082 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009082 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell @@ -629,7 +634,7 @@ comment: Note change of name; nearly all somatic cells can present antigens to T subset: blood_and_immune_upper_slim subset: cellxgene_subset synonym: "APC" RELATED OMO:0003000 [] -xref: ZFA:0009088 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II @@ -642,7 +647,7 @@ def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 -xref: ZFA:0009090 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009090 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -658,7 +663,7 @@ xref: CALOHA:TS-0613 xref: FMA:70545 xref: MESH:D008544 xref: VHOG:0001679 -xref: ZFA:0009091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome @@ -691,7 +696,7 @@ name: exocrine cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] subset: general_cell_types_upper_slim xref: FMA:16014 -xref: ZFA:0009092 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland @@ -706,7 +711,7 @@ subset: general_cell_types_upper_slim subset: human_reference_atlas synonym: "endocrinocyte" EXACT [] xref: FMA:83809 -xref: ZFA:0009096 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0000949 ! endocrine system property_value: RO:0002175 NCBITaxon:9606 @@ -728,14 +733,14 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000188 @@ -748,7 +753,7 @@ synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 -xref: ZFA:0009115 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue @@ -769,7 +774,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -795,27 +800,27 @@ def: "A cell specialized to detect and transduce light." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 -xref: FBbt:00004211 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 -xref: ZFA:0009127 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -827,7 +832,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -839,7 +844,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -849,7 +854,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -884,7 +889,7 @@ subset: cellxgene_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 -xref: ZFA:0009140 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009140 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000473 ! defensive cell @@ -907,7 +912,7 @@ xref: CALOHA:TS-0587 xref: FMA:63261 xref: FMA:83585 xref: MESH:D008264 -xref: ZFA:0009141 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009141 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte @@ -935,7 +940,7 @@ xref: CALOHA:TS-0068 xref: FMA:62869 xref: MESH:D001402 xref: VHOG:0001480 -xref: ZFA:0009142 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009142 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity @@ -963,7 +968,7 @@ is_a: CL:0000000 ! cell [Term] id: CL:0000327 name: extracellular matrix secreting cell -xref: ZFA:0009162 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000499 ! stromal cell [Term] @@ -971,7 +976,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -982,7 +987,7 @@ id: CL:0000349 name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] subset: general_cell_types_upper_slim -xref: ZFA:0009176 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure @@ -1000,7 +1005,7 @@ name: multi-potent skeletal muscle stem cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. xref: FMA:86767 -xref: ZFA:0009179 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009179 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell is_a: CL:0000188 ! cell of skeletal muscle intersection_of: CL:0000048 ! multi fate stem cell @@ -1025,14 +1030,14 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1048,7 +1053,7 @@ xref: BTO:0002042 xref: CALOHA:TS-0194 xref: FMA:83036 xref: MESH:D003713 -xref: ZFA:0009209 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell intersection_of: CL:0000738 ! leukocyte @@ -1089,7 +1094,7 @@ subset: general_cell_types_upper_slim subset: human_reference_atlas xref: BTO:0002064 xref: FMA:83624 -xref: ZFA:0009226 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -1102,7 +1107,7 @@ subset: cellxgene_subset synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 -xref: ZFA:0009234 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009234 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast intersection_of: CL:0000056 ! myoblast @@ -1118,7 +1123,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -1130,7 +1135,7 @@ name: skeletal muscle myoblast def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 -xref: ZFA:0009236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000056 ! myoblast @@ -1153,7 +1158,7 @@ def: "A neuron which conveys sensory information centrally from the periphery." subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 -xref: ZFA:0009238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -1162,7 +1167,7 @@ id: CL:0000527 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:D009476] synonym: "output neuron" EXACT [] -xref: ZFA:0009239 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -1176,16 +1181,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1195,7 +1200,7 @@ def: "A cell that originates from the neural crest and differentiates into a pig comment: Derived from UBERON:0002342 neural crest. xref: BTO:0003217 xref: FMA:83377 -xref: ZFA:0009249 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -1212,7 +1217,7 @@ xref: CALOHA:TS-0583 xref: FMA:62863 xref: MESH:D008214 xref: VHOG:0001535 -xref: ZFA:0009250 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009250 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -1240,7 +1245,7 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] -xref: ZFA:0009251 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell @@ -1272,7 +1277,7 @@ subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0004657 xref: FMA:83551 -xref: ZFA:0009253 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -1291,7 +1296,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1315,7 +1320,7 @@ subset: human_reference_atlas xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 -xref: ZFA:0009265 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009265 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0011026 ! progenitor cell @@ -1347,7 +1352,7 @@ xref: FMA:63147 xref: FMA:83601 xref: MESH:D007694 xref: VHOG:0001697 -xref: ZFA:0009278 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001067 ! group 1 innate lymphoid cell intersection_of: CL:0001067 ! group 1 innate lymphoid cell intersection_of: capable_of GO:0002228 ! natural killer cell mediated immunity @@ -1368,7 +1373,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1381,7 +1386,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1394,7 +1399,7 @@ def: "Muscle cell which has as its direct parts myofilaments organized into sarc xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 -xref: ZFA:0005784 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005784 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0001410 ! striated @@ -1417,7 +1422,7 @@ xref: CALOHA:TS-0549 xref: FMA:62852 xref: MESH:D007962 xref: NCIT:C12529 -xref: ZFA:0009309 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009309 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell @@ -1449,7 +1454,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 xref: MESH:D032383 -xref: ZFA:0009316 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000737 ! striated muscle cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000187 ! muscle cell @@ -1470,7 +1475,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1481,7 +1486,7 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009326 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte @@ -1516,7 +1521,7 @@ synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] -xref: ZFA:0009348 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein @@ -1550,7 +1555,7 @@ synonym: "progenitor B lymphocyte" EXACT [] synonym: "progenitor B-cell" EXACT [] synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 -xref: ZFA:0009349 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 @@ -1572,7 +1577,7 @@ synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] synonym: "progenitor T cell" EXACT [] synonym: "TN1 cell" NARROW [] -xref: ZFA:0009350 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009350 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation @@ -1591,7 +1596,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -1638,7 +1643,7 @@ synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 xref: FMA:70338 -xref: ZFA:0009355 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009355 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1657,7 +1662,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1676,7 +1681,7 @@ synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 xref: CALOHA:TS-0768 xref: FMA:86713 -xref: ZFA:0009357 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009357 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte @@ -1704,7 +1709,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1744,8 +1749,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 creation_date: 2011-11-16T04:28:16Z [Term] @@ -1779,7 +1784,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1799,9 +1804,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:20:48Z" xsd:dateTime [Term] id: CL:0001067 @@ -1812,9 +1817,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032609 ! type II interferon production -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:42:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:42:44Z" xsd:dateTime [Term] id: CL:0002009 @@ -1831,7 +1836,7 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -1845,7 +1850,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1859,7 +1864,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1867,12 +1872,12 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1888,7 +1893,7 @@ is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -1900,7 +1905,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -1912,7 +1917,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1926,7 +1931,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1937,12 +1942,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1952,9 +1957,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1963,7 +1968,7 @@ name: myotube def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] synonym: "myotubule" EXACT [] synonym: "single cell sarcomere" EXACT [] -xref: FBbt:00005812 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000187 ! muscle cell @@ -1971,7 +1976,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere relationship: bearer_of PATO:0002478 ! transversely striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:13:01Z [Term] @@ -1988,7 +1993,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1998,18 +2003,18 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2044,7 +2049,7 @@ relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -2108,7 +2113,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2129,7 +2134,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2140,7 +2145,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2228,6 +2233,18 @@ synonym: "amoeboid cell migration" EXACT [] synonym: "amoeboidal cell migration" EXACT [] is_a: GO:0016477 ! cell migration +[Term] +id: GO:0001677 +name: formation of translation initiation ternary complex +namespace: biological_process +def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd] +synonym: "translation initiation ternary complex assembly" EXACT [] +is_a: GO:0022618 ! protein-RNA complex assembly +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:0044207 ! translation initiation ternary complex +relationship: part_of GO:0006413 ! translational initiation +relationship: results_in_assembly_of GO:0044207 ! translation initiation ternary complex + [Term] id: GO:0001704 name: formation of primary germ layer @@ -2941,6 +2958,79 @@ subset: goslim_prokaryote subset: goslim_yeast is_a: GO:0006259 ! DNA metabolic process +[Term] +id: GO:0006412 +name: translation +namespace: biological_process +alt_id: GO:0006416 +alt_id: GO:0006453 +alt_id: GO:0043037 +def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_prokaryote +subset: goslim_prokaryote_ribbon +synonym: "protein anabolism" EXACT [] +synonym: "protein biosynthesis" EXACT [] +synonym: "protein biosynthetic process" EXACT [] +synonym: "protein formation" EXACT [] +synonym: "protein synthesis" EXACT [] +synonym: "protein translation" EXACT [] +xref: Wikipedia:Translation_(genetics) +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0019538 ! protein metabolic process +relationship: ends_with GO:0006415 ! translational termination +relationship: has_part GO:0006414 ! translational elongation +relationship: part_of GO:0010467 ! gene expression +relationship: starts_with GO:0006413 ! translational initiation + +[Term] +id: GO:0006413 +name: translational initiation +namespace: biological_process +alt_id: GO:0006440 +alt_id: GO:0006454 +def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] +subset: goslim_yeast +synonym: "biopolymerisation" BROAD [] +synonym: "biopolymerization" BROAD [] +synonym: "protein synthesis initiation" BROAD [] +synonym: "translation initiation" EXACT [] +is_a: GO:0044237 ! cellular metabolic process +relationship: part_of GO:0006412 ! translation +relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex + +[Term] +id: GO:0006414 +name: translational elongation +namespace: biological_process +alt_id: GO:0006442 +alt_id: GO:0006455 +def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] +subset: goslim_yeast +synonym: "protein synthesis elongation" BROAD [] +synonym: "translation elongation" EXACT [] +is_a: GO:0009059 ! macromolecule biosynthetic process +relationship: part_of GO:0006412 ! translation + +[Term] +id: GO:0006415 +name: translational termination +namespace: biological_process +alt_id: GO:0006443 +alt_id: GO:0006456 +def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] +synonym: "protein synthesis termination" BROAD [] +synonym: "translation termination" EXACT [] +synonym: "translational complex disassembly" EXACT [] +is_a: GO:0032984 ! protein-containing complex disassembly +relationship: part_of GO:0006412 ! translation + [Term] id: GO:0006810 name: transport @@ -2982,7 +3072,7 @@ name: exocytosis namespace: biological_process alt_id: GO:0016194 alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] +def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] synonym: "vesicle exocytosis" EXACT [] @@ -3334,7 +3424,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3740,6 +3829,36 @@ relationship: has_part GO:0001508 ! action potential relationship: has_part GO:0007268 ! chemical synaptic transmission relationship: part_of GO:0007154 ! cell communication +[Term] +id: GO:0019538 +name: protein metabolic process +namespace: biological_process +alt_id: GO:0006411 +alt_id: GO:0044267 +alt_id: GO:0044268 +def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +subset: goslim_mouse +subset: goslim_pir +subset: goslim_plant +subset: goslim_plant_ribbon +synonym: "cellular protein metabolic process" EXACT [] +synonym: "cellular protein metabolism" EXACT [] +synonym: "multicellular organismal protein metabolic process" NARROW [] +synonym: "protein metabolic process and modification" EXACT [] +synonym: "protein metabolism" EXACT [] +synonym: "protein metabolism and modification" EXACT [] +xref: Wikipedia:Protein_metabolism +is_a: GO:0044238 ! primary metabolic process +intersection_of: GO:0008152 ! metabolic process +intersection_of: has_primary_input_or_output PR:000000001 ! protein +relationship: has_primary_input_or_output PR:000000001 ! protein +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI + [Term] id: GO:0019724 name: B cell mediated immunity @@ -3781,6 +3900,24 @@ relationship: part_of GO:0007399 ! nervous system development relationship: part_of GO:0043009 ! chordate embryonic development relationship: results_in_development_of UBERON:0001049 ! neural tube +[Term] +id: GO:0022411 +name: cellular component disassembly +namespace: biological_process +alt_id: GO:0071845 +def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "cell structure disassembly" EXACT [] +synonym: "cellular component disassembly at cellular level" EXACT [] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_disassembly_of GO:0005575 ! cellular_component +disjoint_from: GO:0022607 ! cellular component assembly +relationship: results_in_disassembly_of GO:0005575 ! cellular_component +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI + [Term] id: GO:0022414 name: reproductive process @@ -3813,6 +3950,48 @@ intersection_of: GO:0003008 ! system process intersection_of: part_of GO:0007586 ! digestion relationship: part_of GO:0007586 ! digestion +[Term] +id: GO:0022607 +name: cellular component assembly +namespace: biological_process +alt_id: GO:0071844 +def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] +subset: goslim_chembl +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_pir +synonym: "cell structure assembly" EXACT [] +synonym: "cellular component assembly at cellular level" EXACT [] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_assembly_of GO:0005575 ! cellular_component +relationship: part_of GO:0044085 ! cellular component biogenesis +relationship: results_in_assembly_of GO:0005575 ! cellular_component + +[Term] +id: GO:0022613 +name: ribonucleoprotein complex biogenesis +namespace: biological_process +def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex." [GOC:isa_complete, GOC:mah] +synonym: "ribonucleoprotein complex biogenesis and assembly" EXACT [GOC:mah] +synonym: "RNA-protein complex biogenesis" EXACT [GOC:mah] +is_a: GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0022618 +name: protein-RNA complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl] +subset: goslim_chembl +synonym: "ribonucleoprotein complex assembly" EXACT [] +synonym: "RNA-protein complex assembly" EXACT [] +synonym: "RNP complex assembly" EXACT [] +is_a: GO:0065003 ! protein-containing complex assembly +is_a: GO:0071826 ! protein-RNA complex organization +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex +relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis +relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex + [Term] id: GO:0023052 name: signaling @@ -3875,7 +4054,7 @@ relationship: part_of GO:0030016 ! myofibril id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -3890,7 +4069,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -4237,6 +4416,25 @@ xref: Wikipedia:Secretion is_a: GO:0046903 ! secretion is_a: GO:0140352 ! export from cell +[Term] +id: GO:0032984 +name: protein-containing complex disassembly +namespace: biological_process +alt_id: GO:0034623 +alt_id: GO:0043241 +alt_id: GO:0043624 +def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] +synonym: "cellular macromolecule complex disassembly" RELATED [] +synonym: "cellular protein complex disassembly" RELATED [] +synonym: "macromolecule complex disassembly" RELATED [] +synonym: "protein complex disassembly" EXACT [] +is_a: GO:0022411 ! cellular component disassembly +is_a: GO:0043933 ! protein-containing complex organization +intersection_of: GO:0022411 ! cellular component disassembly +intersection_of: results_in_disassembly_of GO:0032991 ! protein-containing complex +relationship: results_in_disassembly_of GO:0032991 ! protein-containing complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI + [Term] id: GO:0032991 name: protein-containing complex @@ -4443,7 +4641,7 @@ is_a: GO:0042611 ! MHC protein complex id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -4603,6 +4801,53 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27281" xsd:anyURI +[Term] +id: GO:0043933 +name: protein-containing complex organization +namespace: biological_process +alt_id: GO:0034600 +alt_id: GO:0034621 +alt_id: GO:0071822 +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] +synonym: "cellular macromolecular complex organization" RELATED [] +synonym: "cellular macromolecular complex subunit organisation" RELATED [] +synonym: "cellular macromolecular complex subunit organization" RELATED [] +synonym: "macromolecular complex organization" RELATED [] +synonym: "macromolecular complex subunit organisation" RELATED [] +synonym: "macromolecular complex subunit organization" RELATED [] +synonym: "protein complex subunit organisation" EXACT [GOC:mah] +synonym: "protein complex subunit organization" EXACT [] +synonym: "protein-containing complex subunit organization" RELATED [] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex +relationship: results_in_organization_of GO:0032991 ! protein-containing complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI +created_by: mah +creation_date: 2010-09-08T10:01:42Z + +[Term] +id: GO:0044085 +name: cellular component biogenesis +namespace: biological_process +alt_id: GO:0071843 +def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: goslim_pir +synonym: "cellular component biogenesis at cellular level" EXACT [] +is_a: GO:0071840 ! cellular component organization or biogenesis + +[Term] +id: GO:0044207 +name: translation initiation ternary complex +namespace: cellular_component +def: "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:jl] +synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] +synonym: "translation initiation (ternary) complex" EXACT [] +is_a: GO:1990904 ! ribonucleoprotein complex +relationship: part_of GO:0005737 ! cytoplasm +created_by: jl +creation_date: 2009-10-22T02:38:55Z + [Term] id: GO:0044237 name: cellular metabolic process @@ -4615,6 +4860,21 @@ synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process +[Term] +id: GO:0044238 +name: primary metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] +subset: gocheck_do_not_annotate +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_pir +subset: goslim_plant_ribbon +subset: goslim_prokaryote_ribbon +synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite +is_a: GO:0008152 ! metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI + [Term] id: GO:0044249 name: cellular biosynthetic process @@ -5330,6 +5590,36 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z +[Term] +id: GO:0065003 +name: protein-containing complex assembly +namespace: biological_process +alt_id: GO:0006461 +alt_id: GO:0034622 +alt_id: GO:0043623 +def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_pombe +subset: goslim_prokaryote +synonym: "cellular macromolecule complex assembly" RELATED [] +synonym: "cellular protein complex assembly" EXACT [] +synonym: "cellular protein-containing complex assembly" RELATED [] +synonym: "chaperone activity" RELATED [] +synonym: "macromolecular complex assembly" RELATED [] +synonym: "macromolecule complex assembly" RELATED [] +synonym: "protein complex assembly" RELATED [] +synonym: "protein complex formation" RELATED [] +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0043933 ! protein-containing complex organization +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:0032991 ! protein-containing complex +relationship: results_in_assembly_of GO:0032991 ! protein-containing complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI + [Term] id: GO:0065007 name: biological regulation @@ -5371,18 +5661,21 @@ intersection_of: GO:0030133 ! transport vesicle intersection_of: capable_of GO:0099500 ! vesicle fusion to plasma membrane [Term] -id: GO:0071704 -name: organic substance metabolic process +id: GO:0071826 +name: protein-RNA complex organization namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex." [GOC:mah] +synonym: "protein-RNA complex subunit organization" EXACT [GOC:mah] +synonym: "ribonucleoprotein complex subunit organisation" EXACT [GOC:mah] +synonym: "ribonucleoprotein complex subunit organization" EXACT [] +synonym: "RNA-protein complex subunit organization" EXACT [GOC:mah] +is_a: GO:0043933 ! protein-containing complex organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex +relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI created_by: mah -creation_date: 2010-03-08T03:32:18Z +creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 @@ -5774,27 +6067,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2020-11-11T17:19:06Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1902105 name: regulation of leukocyte differentiation @@ -5840,6 +6112,24 @@ relationship: regulates GO:0030097 ! hemopoiesis created_by: pad creation_date: 2014-12-04T15:34:13Z +[Term] +id: GO:1990904 +name: ribonucleoprotein complex +namespace: cellular_component +alt_id: GO:0030529 +alt_id: GO:1990903 +def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] +subset: goslim_pir +synonym: "extracellular ribonucleoprotein complex" NARROW [] +synonym: "intracellular ribonucleoprotein complex" NARROW [] +synonym: "protein-RNA complex" EXACT [] +synonym: "RNA-protein complex" EXACT [] +synonym: "RNP" EXACT [] +xref: Wikipedia:Ribonucleoprotein +is_a: GO:0032991 ! protein-containing complex +created_by: pr +creation_date: 2015-11-19T12:26:37Z + [Term] id: GO:2000026 name: regulation of multicellular organismal development @@ -6415,7 +6705,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6427,7 +6717,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6437,7 +6727,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6447,7 +6737,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6456,7 +6746,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6469,7 +6759,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6480,7 +6770,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6490,7 +6780,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6502,7 +6792,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:15Z [Term] @@ -6513,7 +6803,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6522,7 +6812,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6576,6 +6866,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -7255,6 +7548,15 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -7306,6 +7608,18 @@ synonym: "CD45R" EXACT [] synonym: "PTPRC/iso:CD45R" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -7342,7 +7656,7 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7357,7 +7671,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7407,7 +7721,7 @@ relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002176 UBERON:0001474 ! connects bone element relationship: RO:0002176 UBERON:0001630 ! connects muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI [Term] id: UBERON:0000058 @@ -7420,7 +7734,7 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7466,7 +7780,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7785,7 +8099,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -7887,7 +8201,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -7911,7 +8225,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -7934,7 +8248,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -7994,7 +8308,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8029,7 +8343,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8057,7 +8371,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8082,7 +8396,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8119,7 +8433,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -8173,7 +8487,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8217,7 +8531,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8253,7 +8567,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8273,7 +8587,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -8299,7 +8613,7 @@ xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 -xref: FBbt:00005835 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005835 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 @@ -8335,7 +8649,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8370,7 +8684,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8403,7 +8717,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8426,7 +8740,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000486 @@ -8502,7 +8816,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -8523,7 +8837,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -8543,7 +8857,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8577,7 +8891,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8595,7 +8909,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8615,7 +8929,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8632,8 +8946,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8659,7 +8973,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8676,7 +8990,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -8699,7 +9013,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8712,7 +9026,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -8733,7 +9047,7 @@ xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 -xref: FBbt:00005068 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005068 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9668 xref: GAID:439 xref: MA:0000012 @@ -8778,7 +9092,7 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -8851,7 +9165,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -8905,7 +9219,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -8944,7 +9258,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -8970,7 +9284,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9000,8 +9314,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -9032,7 +9346,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9078,7 +9392,7 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007692 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9093,7 +9407,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001049 @@ -9132,7 +9446,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9148,7 +9462,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9241,7 +9555,7 @@ intersection_of: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle f relationship: part_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: RO:0002202 UBERON:0003082 ! develops from myotome relationship: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string [Term] @@ -9356,7 +9670,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -9447,7 +9761,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -9619,7 +9933,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -9660,7 +9974,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -9727,8 +10041,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -9751,7 +10065,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -9826,7 +10140,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0000949 ! endocrine system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI [Term] id: UBERON:0002371 @@ -9871,7 +10185,7 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -10070,7 +10384,7 @@ xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 xref: EMAPA:18425 -xref: FBbt:00100317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7146 xref: FMA:86294 xref: galen:Gland @@ -10087,7 +10401,7 @@ is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: produces UBERON:0000463 ! organism substance relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] id: UBERON:0002532 @@ -10111,7 +10425,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -10210,7 +10524,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -10245,7 +10559,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -10276,7 +10590,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -10311,7 +10625,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003082 @@ -10348,7 +10662,7 @@ xref: ZFA:0001056 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome relationship: RO:0002433 UBERON:0001630 ! contributes to morphology of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI property_value: IAO:0000116 "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string [Term] @@ -10405,7 +10719,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -10434,7 +10748,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -10598,7 +10912,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -10696,7 +11010,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -10712,7 +11026,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -10848,7 +11162,7 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000970 ! eye @@ -10868,7 +11182,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -11253,7 +11567,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -11323,7 +11637,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -11549,7 +11863,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -11702,7 +12016,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -11759,8 +12073,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Term] id: UBERON:8600006 @@ -11770,8 +12084,8 @@ def: "A striated muscle tissue that is associated with soft internal organs (vis synonym: "striated visceral muscle tissue" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:8600004 ! visceral muscle tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:34:43Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:34:43Z" xsd:dateTime [Typedef] id: BFO:0000067 @@ -12842,8 +13156,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -12851,8 +13165,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -12861,8 +13175,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -13013,16 +13327,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -13031,6 +13349,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -13048,6 +13367,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -13266,6 +13586,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -13724,18 +14045,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/src/ontology/subsets/general_cell_types_upper_slim.owl b/src/ontology/subsets/general_cell_types_upper_slim.owl index 7d5d68045..4354de63c 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.owl +++ b/src/ontology/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4506,6 +4512,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4517,6 +4525,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4527,6 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4539,6 +4549,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4557,6 +4568,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4586,6 +4598,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4694,6 +4707,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4705,6 +4719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4716,6 +4731,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -10052,7 +10068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A connective tissue cell found in bone. - 2011-11-16T04:28:16Z + 2011-11-16T04:28:16Z bone cell @@ -10204,7 +10220,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative @@ -10369,7 +10385,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. - 2010-01-19T02:51:58Z + 2010-01-19T02:51:58Z MDP macrophage dendritic cell progenitor @@ -10420,7 +10436,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -10463,7 +10479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10502,7 +10518,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -10546,7 +10562,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. - 2010-07-22T04:48:15Z + 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 @@ -10593,7 +10609,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell involved in the formation of a monocyte (monopoiesis). - 2010-08-30T01:27:48Z + 2010-08-30T01:27:48Z FMA:83552 monopoietic cell @@ -10635,7 +10651,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -10671,7 +10687,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -10710,7 +10726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -10740,7 +10756,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -10794,7 +10810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. - 2010-09-24T01:13:01Z + 2010-09-24T01:13:01Z FBbt:00005812 myotubule single cell sarcomere @@ -10841,7 +10857,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -10865,7 +10881,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). - 2012-06-15T02:51:27Z + 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -10903,7 +10919,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -11264,7 +11280,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. - 2010-05-25T01:36:34Z + 2010-05-25T01:36:34Z neutrophillic cytoplasm @@ -11299,7 +11315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -11507,6 +11523,48 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + translation initiation ternary complex assembly + biological_process + GO:0001677 + formation of translation initiation ternary complex + + + + + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + GOC:hjd + + + + @@ -12821,32 +12879,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -13358,6 +13416,164 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. + GO:0006416 + GO:0006453 + GO:0043037 + Wikipedia:Translation_(genetics) + protein anabolism + protein biosynthesis + protein biosynthetic process + protein formation + protein synthesis + protein translation + biological_process + GO:0006412 + + + + + + + + + + translation + + + + + The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. + GO:0006440 + GO:0006454 + biopolymerisation + biopolymerization + protein synthesis initiation + translation initiation + biological_process + GO:0006413 + + translational initiation + + + + + The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. + ISBN:019879276X + + + + + + + + + + + + + + + The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. + GO:0006442 + GO:0006455 + protein synthesis elongation + translation elongation + biological_process + GO:0006414 + + translational elongation + + + + + The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. + GOC:ems + + + + + + + + + + + + + + + The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). + GO:0006443 + GO:0006456 + protein synthesis termination + translation termination + translational complex disassembly + biological_process + GO:0006415 + translational termination + + + + + The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). + GOC:hjd + ISBN:019879276X + + + + @@ -13446,7 +13662,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0016194 GO:0016195 Wikipedia:Exocytosis @@ -13460,7 +13676,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GOC:mah ISBN:0716731363 PMID:22323285 @@ -14245,7 +14461,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -15265,6 +15480,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving a protein. Includes protein modification. + https://github.com/geneontology/go-ontology/issues/23112 + https://github.com/geneontology/go-ontology/issues/27189 + GO:0006411 + GO:0044267 + GO:0044268 + Wikipedia:Protein_metabolism + cellular protein metabolic process + cellular protein metabolism + protein metabolic process and modification + protein metabolism + protein metabolism and modification + multicellular organismal protein metabolic process + biological_process + GO:0019538 + + + + + + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + protein metabolic process + + + + + The chemical reactions and pathways involving a protein. Includes protein modification. + GOC:ma + + + + @@ -15387,6 +15657,49 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + A cellular process that results in the breakdown of a cellular component. + https://github.com/geneontology/go-ontology/issues/27189 + GO:0071845 + cell structure disassembly + cellular component disassembly at cellular level + biological_process + GO:0022411 + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cellular component disassembly + + + + + A cellular process that results in the breakdown of a cellular component. + GOC:isa_complete + + + + @@ -15458,6 +15771,132 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + The aggregation, arrangement and bonding together of a cellular component. + GO:0071844 + cell structure assembly + cellular component assembly at cellular level + biological_process + GO:0022607 + + + + cellular component assembly + + + + + The aggregation, arrangement and bonding together of a cellular component. + GOC:isa_complete + + + + + + + + + A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. + RNA-protein complex biogenesis + ribonucleoprotein complex biogenesis and assembly + biological_process + GO:0022613 + ribonucleoprotein complex biogenesis + + + + + A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. + GOC:isa_complete + GOC:mah + + + + + RNA-protein complex biogenesis + GOC:mah + + + + + ribonucleoprotein complex biogenesis and assembly + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. + RNA-protein complex assembly + RNP complex assembly + ribonucleoprotein complex assembly + biological_process + GO:0022618 + + protein-RNA complex assembly + + + + + The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. + GOC:jl + + + + @@ -15644,7 +16083,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -15685,7 +16124,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -16566,6 +17004,50 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The disaggregation of a protein-containing macromolecular complex into its constituent components. + https://github.com/geneontology/go-ontology/issues/22580 + GO:0034623 + GO:0043241 + GO:0043624 + protein complex disassembly + biological_process + cellular macromolecule complex disassembly + cellular protein complex disassembly + macromolecule complex disassembly + GO:0032984 + protein-containing complex disassembly + + + + + The disaggregation of a protein-containing macromolecular complex into its constituent components. + GOC:mah + + + + @@ -17172,7 +17654,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -17568,6 +18050,112 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. + https://github.com/geneontology/go-ontology/issues/22580 + mah + 2010-09-08T10:01:42Z + GO:0034600 + GO:0034621 + GO:0071822 + protein complex subunit organisation + protein complex subunit organization + biological_process + cellular macromolecular complex organization + cellular macromolecular complex subunit organisation + cellular macromolecular complex subunit organization + macromolecular complex organization + macromolecular complex subunit organisation + macromolecular complex subunit organization + protein-containing complex subunit organization + GO:0043933 + protein-containing complex organization + + + + + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. + GOC:mah + + + + + protein complex subunit organisation + GOC:mah + + + + + + + + + A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + GO:0071843 + cellular component biogenesis at cellular level + biological_process + GO:0044085 + + cellular component biogenesis + + + + + A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + GOC:jl + GOC:mah + + + + + + + + + + + + + + + A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + jl + 2009-10-22T02:38:55Z + translation initiation (ternary) complex + Met-tRNA/eIF2.GTP ternary complex + cellular_component + GO:0044207 + translation initiation ternary complex + + + + + A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + GOC:jl + + + + @@ -17597,6 +18185,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. + https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite + primary metabolism + biological_process + GO:0044238 + + + + + + primary metabolic process + + + + + The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. + GOC:go_curators + + + + @@ -19557,6 +20171,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. + https://github.com/geneontology/go-ontology/issues/22580 + GO:0006461 + GO:0034622 + GO:0043623 + cellular protein complex assembly + biological_process + cellular macromolecule complex assembly + cellular protein-containing complex assembly + chaperone activity + macromolecular complex assembly + macromolecule complex assembly + protein complex assembly + protein complex formation + GO:0065003 + + + + + + + + protein-containing complex assembly + + + + + The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. + GOC:jl + + + + @@ -19681,26 +20350,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 + + + + + + + + + + + + + + + + + + + + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. + https://github.com/geneontology/go-ontology/issues/25143 mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism + 2010-09-08T10:10:35Z + RNA-protein complex subunit organization + protein-RNA complex subunit organization + ribonucleoprotein complex subunit organisation + ribonucleoprotein complex subunit organization biological_process - GO:0071704 - - organic substance metabolic process + GO:0071826 + protein-RNA complex organization - + - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. + GOC:mah + + + + + RNA-protein complex subunit organization + GOC:mah + + + + + protein-RNA complex subunit organization + GOC:mah + + + + + ribonucleoprotein complex subunit organisation GOC:mah @@ -20852,63 +21556,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -21073,6 +21720,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A macromolecular complex that contains both RNA and protein molecules. + pr + 2015-11-19T12:26:37Z + GO:0030529 + GO:1990903 + Wikipedia:Ribonucleoprotein + RNA-protein complex + RNP + protein-RNA complex + extracellular ribonucleoprotein complex + intracellular ribonucleoprotein complex + cellular_component + GO:1990904 + + ribonucleoprotein complex + + + + + A macromolecular complex that contains both RNA and protein molecules. + GOC:krc + GOC:vesicles + + + + @@ -22739,6 +23416,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -24550,6 +25235,39 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -24724,6 +25442,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -24927,8 +25697,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -24976,11 +25746,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -24993,13 +25763,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + AEO @@ -25904,7 +26674,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25940,14 +26710,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -27354,7 +28124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27396,14 +28166,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27746,7 +28516,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27781,14 +28551,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27828,7 +28598,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27863,14 +28633,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27911,7 +28681,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27952,14 +28722,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28215,8 +28985,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -28248,24 +29018,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -28659,7 +29429,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28711,14 +29481,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -28784,7 +29554,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -28829,7 +29599,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -28843,7 +29613,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -29563,7 +30333,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Skeletal element that is composed of bone tissue. @@ -29605,14 +30375,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -29678,7 +30448,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -29715,14 +30485,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -30251,9 +31021,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -30301,15 +31071,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -30328,19 +31098,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -30380,8 +31150,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -30419,11 +31189,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -30436,13 +31206,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -30567,22 +31337,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -30615,45 +31385,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -30960,7 +31730,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31016,14 +31786,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -31235,7 +32005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31289,14 +32059,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -31706,7 +32476,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -31729,14 +32499,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -31890,9 +32660,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -31921,34 +32691,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -31988,7 +32758,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -32014,7 +32784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32027,7 +32797,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -32074,7 +32844,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32114,7 +32884,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32127,7 +32897,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -32177,7 +32947,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32218,7 +32988,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -32231,7 +33001,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2-abduced @@ -32391,7 +33161,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -32406,14 +33176,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -32715,7 +33485,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The bilaminar epithelium formed from the myotome and dermatome. AAO:0010572 AEO:0000214 @@ -32733,7 +33503,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004290 dermomyotome - + @@ -32752,7 +33522,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 ZFA @@ -33083,7 +33853,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -33097,14 +33867,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -33131,7 +33901,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33170,14 +33940,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -33618,7 +34388,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -33634,14 +34404,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -33950,7 +34720,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -33964,7 +34734,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -33977,7 +34747,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -34005,7 +34775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -34022,14 +34792,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -34640,7 +35410,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34666,7 +35436,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -34682,7 +35452,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -34731,7 +35501,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -34739,7 +35509,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -34752,7 +35522,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -34910,7 +35680,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34927,14 +35697,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -34956,7 +35726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -34964,14 +35734,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -35451,7 +36221,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35475,7 +36245,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0011899 epimysium - + @@ -35488,7 +36258,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -35594,7 +36364,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35615,7 +36385,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -35628,7 +36398,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -36183,7 +36953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36206,7 +36976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -36219,7 +36989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -36305,7 +37075,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36322,14 +37092,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal musculature - + - + MA @@ -36882,5 +37652,5 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + diff --git a/src/ontology/subsets/general_cell_types_upper_slim.tsv b/src/ontology/subsets/general_cell_types_upper_slim.tsv index df42d0949..e12af28b8 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.tsv +++ b/src/ontology/subsets/general_cell_types_upper_slim.tsv @@ -1,270 +1,279 @@ ?x ?label -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1005 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1012 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1018 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1059 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1074 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+_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid857 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid864 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid874 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid901 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid918 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid927 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid977 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid985 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid993 "cell" "neuronal receptor cell" "early embryonic cell (metazoa)" @@ -400,6 +409,7 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "heterochromatin" "action potential" "ameboidal-type cell migration" + "formation of translation initiation ternary complex" "formation of primary germ layer" "ectoderm formation" "endoderm formation" @@ -452,6 +462,10 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "cell-cell junction" "DNA metabolic process" "DNA recombination" + "translation" + "translational initiation" + "translational elongation" + "translational termination" "transport" "monoatomic ion transport" "exocytosis" @@ -511,11 +525,16 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "cell migration" "stem cell division" "transmission of nerve impulse" + "protein metabolic process" "B cell mediated immunity" "antigen processing and presentation" "neural tube development" + "cellular component disassembly" "reproductive process" "digestive system process" + "cellular component assembly" + "ribonucleoprotein complex biogenesis" + "protein-RNA complex assembly" "signaling" "signal release" "myofibril" @@ -546,6 +565,7 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "developmental process" "type II interferon production" "secretion by cell" + "protein-containing complex disassembly" "protein-containing complex" "protein-DNA complex" "V(D)J recombination" @@ -576,7 +596,11 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "intracellular non-membrane-bounded organelle" "organelle lumen" "contractile muscle fiber" + "protein-containing complex organization" + "cellular component biogenesis" + "translation initiation ternary complex" "cellular metabolic process" + "primary metabolic process" "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" "innate immune response" @@ -633,11 +657,12 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "membrane organization" "membrane fusion" "collagen-containing extracellular matrix" + "protein-containing complex assembly" "biological regulation" "intracellular organelle lumen" "anchoring junction" "exocytic vesicle" - "organic substance metabolic process" + "protein-RNA complex organization" "cellular component organization or biogenesis" "cell periphery" "elastic fiber" @@ -671,10 +696,10 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "exocytic process" "export from cell" "defense response to symbiont" - "organic substance biosynthetic process" "regulation of leukocyte differentiation" "mononuclear cell differentiation" "regulation of hemopoiesis" + "ribonucleoprotein complex" "regulation of multicellular organismal development" "root" "Muridae" @@ -800,11 +825,13 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "nuclear factor NF-kappa-B p100 subunit" "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "eukaryotic protein" "cathepsin-like protease" "receptor-type tyrosine-protein phosphatase C isoform CD45R" + "protein-containing molecular entity" "processual entity" "sense organ" "tube" diff --git a/src/ontology/subsets/kidney_upper_slim.json b/src/ontology/subsets/kidney_upper_slim.json index 083c32f0b..a1c0d3fe7 100644 --- a/src/ontology/subsets/kidney_upper_slim.json +++ b/src/ontology/subsets/kidney_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/kidney_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -548,24 +395,6 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000064", - "lbl" : "ciliated cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell that has a filiform extrusion of the cell surface.", - "xrefs" : [ "GOC:tfm" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "xrefs" : [ { - "val" : "VHOG:0001532" - }, { - "val" : "XAO:0000031" - }, { - "val" : "ZFA:0009032" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000066", "lbl" : "epithelial cell", @@ -603,22 +432,6 @@ "val" : "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000067", - "lbl" : "ciliated epithelial cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An epithelial cell that has a cilia.", - "xrefs" : [ "GOC:tfm" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "xrefs" : [ { - "val" : "FMA:70605" - }, { - "val" : "ZFA:0009035" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000068", "lbl" : "duct epithelial cell", @@ -643,10 +456,6 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cuboidal endothelial cell of vascular tree" - } ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -1084,15 +893,6 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000239", - "lbl" : "brush border epithelial cell", - "type" : "CLASS", - "meta" : { - "xrefs" : [ { - "val" : "ZFA:0009143" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000255", "lbl" : "eukaryotic cell", @@ -1627,9 +1427,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000666", - "lbl" : "fenestrated cell", + "lbl" : "fenestrated endothelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.", + "xrefs" : [ "DOI:10.1007/978-3-211-99390-3_133" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -2101,6 +1905,7 @@ "val" : "An epithelial cell of the proximal tubule of the kidney.", "xrefs" : [ "GOC:tfm", "ISBN:1-4160-2328-3" ] }, + "comments" : [ "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -2968,30 +2773,6 @@ "val" : "2022-11-30T14:35:08Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_4033054", "lbl" : "perivascular cell", @@ -3009,68 +2790,6 @@ "val" : "2023-08-22T13:40:28Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0000226", - "lbl" : "microtubule cytoskeleton organization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pombe" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "microtubule cytoskeleton organisation", - "xrefs" : [ "GOC:mah" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "microtubule cytoskeleton organization and biogenesis", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23114" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23195" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -3078,7 +2797,7 @@ "meta" : { "definition" : { "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", - "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + "xrefs" : [ "GOC:mah", "ISBN:0815316194" ] }, "comments" : [ "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -3209,24 +2928,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0001578", - "lbl" : "microtubule bundle formation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process that results in a parallel arrangement of microtubules.", - "xrefs" : [ "GOC:dph" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "microtubule bundling" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0001677", "lbl" : "formation of translation initiation ternary complex", @@ -4081,85 +3782,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005773", - "lbl" : "vacuole", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.", - "xrefs" : [ "GOC:mtg_sensu", "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar carboxypeptidase Y" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Vacuole" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005794", - "lbl" : "Golgi apparatus", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "comments" : [ "Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "Golgi" - }, { - "pred" : "hasExactSynonym", - "val" : "Golgi complex" - }, { - "pred" : "hasNarrowSynonym", - "val" : "Golgi ribbon" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao451912436" - }, { - "val" : "Wikipedia:Golgi_apparatus" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005798", - "lbl" : "Golgi-associated vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this definition includes vesicles that are transiently associated with the Golgi." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Golgi vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vesicular component", - "xrefs" : [ "NIF_Subcellular:sao138219748" ] - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao819927218" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0005840", "lbl" : "ribosome", @@ -4195,55 +3817,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005856", - "lbl" : "cytoskeleton", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. 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The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. 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The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. 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Docking requires only that the proteins come close enough to interact and adhere.", - "xrefs" : [ "GOC:isa_complete", "PMID:27875684" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0022411", "lbl" : "cellular component disassembly", @@ -6510,7 +5795,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -6540,7 +5825,7 @@ "meta" : { "definition" : { "val" : "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:18391171" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6562,7 +5847,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -6780,47 +6065,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030705", - "lbl" : "cytoskeleton-dependent intracellular transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030990", - "lbl" : "intraciliary transport particle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.", - "xrefs" : [ "GOC:cilia", "GOC:kmv", "PMID:14570576", "PMID:22118932", "PMID:23945166" ] - }, - "comments" : [ "Note that we deem cilia and microtubule-based flagella to be equivalent." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport complex" - }, { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport particle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "IFT complex" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0031012", "lbl" : "extracellular matrix", @@ -6851,81 +6095,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031410", - "lbl" : "cytoplasmic vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A vesicle found in the cytoplasm of a cell.", - "xrefs" : [ "GOC:ai", "GOC:mah", "GOC:vesicles" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane bounded vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane-enclosed vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic, membrane-bounded vesicle" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao180601769" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031503", - "lbl" : "protein-containing complex localization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "establishment and maintenance of protein complex localization" - 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} }, { "id" : "http://purl.obolibrary.org/obo/GO_0031974", "lbl" : "membrane-enclosed lumen", @@ -7122,20 +6291,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032838", - "lbl" : "plasma membrane bounded cell projection cytoplasm", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection.", - "xrefs" : [ "GOC:krc", "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032940", "lbl" : "secretion by cell", @@ -7272,29 +6427,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033365", - "lbl" : "protein localization to organelle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process in which a protein is transported to, or maintained in, a location within an organelle.", - 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"comments" : [ "Note that cilia and eukaryotic flagella are deemed to be equivalent." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ciliary axoneme assembly" - }, { - "pred" : "hasExactSynonym", - "val" : "cilium axoneme assembly" - }, { - "pred" : "hasExactSynonym", - "val" : "flagellar axoneme assembly" - }, { - "pred" : "hasExactSynonym", - "val" : "flagellum axoneme assembly" - }, { - "pred" : "hasRelatedSynonym", - "val" : "axoneme biogenesis", - "xrefs" : [ "GOC:mah" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cilium axoneme biogenesis", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035083" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035084" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0035148", "lbl" : "tube formation", @@ -7471,70 +6561,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0035735", - "lbl" : "intraciliary transport involved in cilium assembly", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.", - "xrefs" : [ "GOC:bf", "GOC:cilia", "Reactome:R-HSA-5620924.2" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "intraflagellar transport" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intraciliary transport involved in cilium morphogenesis" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intraflagellar transport involved in cilium morphogenesis" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-5620924.2" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-03-17T10:55:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0035869", - "lbl" : "ciliary transition zone", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. 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Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cilial transition zone" - }, { - "pred" : "hasExactSynonym", - "val" : "cilium transition zone" - }, { - "pred" : "hasRelatedSynonym", - "val" : "connecting cilium" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-05-25T03:09:58Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0040011", "lbl" : "locomotion", @@ -7582,58 +6608,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042073", - "lbl" : "intraciliary transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.", - "xrefs" : [ "GOC:cilia", "GOC:kmv", "PMID:17981739", "PMID:18180368", "PMID:22869374", "Reactome:R-HSA-5620924.2" ] - }, - "comments" : [ "Note that we deem cilium and microtubule-based flagellum to be equivalent." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport" - }, { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport involved in cilium organization" - }, { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport involved in microtubule-based flagellum organisation" - }, { - "pred" : "hasRelatedSynonym", - "val" : "IFT" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Intraflagellar_transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3176" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3312" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3378" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3398" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4890" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_5782" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035734" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0042391", "lbl" : "regulation of membrane potential", @@ -7698,7 +6672,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -8096,13 +7070,16 @@ "meta" : { "definition" : { "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", - "xrefs" : [ "GOC:go_curators", "http://www.metacyc.org" ] + "xrefs" : [ "GOC:go_curators" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "primary metabolism" } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" @@ -8143,32 +7120,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044782", - "lbl" : "cilium organization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. 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Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). 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In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.", - "xrefs" : [ "GOC:cilia", "PMID:13978319", "PMID:23348840", "PMID:23530209", "PMID:25686250", "PMID:26981235", "Reactome:R-HSA-5620912.1" ] - }, - "comments" : [ "Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ciliary basal body docking" - }, { - "pred" : "hasRelatedSynonym", - "val" : "anchoring of the basal body to the plasma membrane" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-5620912.1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-08-05T16:12:33Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0097712", - "lbl" : "vesicle targeting, trans-Golgi to periciliary membrane compartment", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.", - "xrefs" : [ "GOC:cilia", "PMID:20106869", "PMID:23351793", "PMID:24814148", "PMID:26485645", "Reactome:R-HSA-5620920.1" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-08-05T16:16:28Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0097734", "lbl" : "extracellular exosome biogenesis", @@ -10321,55 +8781,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099111", - "lbl" : "microtubule-based transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.", - "xrefs" : [ "GOC:cjm", "ISBN:0815316194" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099512", - "lbl" : "supramolecular fiber", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.", - "xrefs" : [ "GOC:dos" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "fibril" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099513", - "lbl" : "polymeric cytoskeletal fiber", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits.", - "xrefs" : [ "GOC:dos" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0099536", "lbl" : "synaptic signaling", @@ -10400,21 +8811,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099568", - "lbl" : "cytoplasmic region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.", - "xrefs" : [ "GOC:dos" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", "lbl" : "cellular anatomical entity", @@ -10544,27 +8940,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140056", - "lbl" : "organelle localization by membrane tethering", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.", - "xrefs" : [ "PMID:27875684" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pombe" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-27T09:58:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140112", "lbl" : "extracellular vesicle biogenesis", @@ -10616,62 +8991,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1903047", "lbl" : "mitotic cell cycle process", @@ -10718,47 +9037,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1905349", - "lbl" : "ciliary transition zone assembly", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone.", - "xrefs" : [ "GOC:TermGenie", "GOC:cilia", "GO_REF:0000079", "PMID:21725307", "PMID:23644468", "PMID:24448408", "PMID:26595381", "PMID:26982032" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cilial transition zone assembly", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cilial transition zone formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "ciliary transition zone formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cilium transition zone assembly", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cilium transition zone formation", - "xrefs" : [ "GOC:TermGenie" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-08-04T14:49:43Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1990904", "lbl" : "ribonucleoprotein complex", @@ -10805,260 +9083,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], - "xrefs" : [ { - "val" : "IAO:0000233" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." - }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -11727,73 +9751,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -12433,6 +10390,27 @@ "val" : "quality" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0002064", + "lbl" : "fenestrated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes.", + "xrefs" : [ "PATOC:me" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/pato#cell_quality", "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2061-091X" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-01T01:46:53Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002078", "lbl" : "hollow", @@ -12517,27 +10495,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002226", - "lbl" : "subcylindrical", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.", - "xrefs" : [ "url:http://www.thefreedictionary.com/Subcylindrical" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-2061-091X" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-07-13T04:22:30Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002266", "lbl" : "3-D shape", @@ -12588,28 +10545,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002309", - "lbl" : "fiber shaped", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter.", - "xrefs" : [ "PATOC:DC" ] - }, - "comments" : [ "Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-2061-091X" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-09-09T04:50:10Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002318", "lbl" : "superelliptic", @@ -13760,6 +11695,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -13836,2941 +11795,6938 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000053" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], "xrefs" : [ { - "val" : "RO:0000056" + "val" : "galen:Tube" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000026", + "lbl" : "appendage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "Major subdivision of an organism that protrudes from the body[DOS, CARO].", + "xrefs" : [ "CARO:DOS" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "appendages", + "xrefs" : [ "XAO:0000218" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "extremitaet", + "xrefs" : [ "BTO:0001492" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "extremity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "limbs/digits/tail", + "xrefs" : [ "MP:0000001" ] + } ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "AEO:0000193" + }, { + "val" : "BILA:0000018" + }, { + "val" : "BTO:0001492" + }, { + "val" : "CARO:0010003" + }, { + "val" : "EFO:0000799" + }, { + "val" : "EHDAA2:0003193" + }, { + "val" : "EMAPA:37283" + }, { + "val" : "EV:0100155" + }, { + "val" : "FBbt:00007000" + }, { + "val" : "HAO:0000144" + }, { + "val" : "MAT:0000023" + }, { + "val" : "MESH:D005121" + }, { + "val" : "MIAA:0000023" + }, { + "val" : "NCIT:C61460" + }, { + "val" : "UMLS:C0598782" + }, { + "val" : "VSAO:0000075" + }, { + "val" : "Wikipedia:Appendage" + }, { + "val" : "XAO:0000218" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000055", + "lbl" : "vessel", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + "val" : "A tubular structure that contains, conveys body fluid, such as blood or lymph.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000056", + "lbl" : "ureter", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.", + "xrefs" : [ "GO:0090189", "Wikipedia:Ureter" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "metanephric duct", + "xrefs" : [ "ISBN:0073040584", "VHOG:0000605" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010254" + }, { + "val" : "BTO:0001409" + }, { + "val" : "CALOHA:TS-1084" + }, { + "val" : "EFO:0000930" + }, { + "val" : "EHDAA2:0002139" + }, { + "val" : "EHDAA:9341" + }, { + "val" : "EMAPA:17950" + }, { + "val" : "EV:0100097" + }, { + "val" : "FMA:9704" + }, { + "val" : "GAID:438" + }, { + "val" : "MA:0000378" + }, { + "val" : "MAT:0000120" + }, { + "val" : "MESH:D014513" + }, { + "val" : "MIAA:0000120" + }, { + "val" : "NCIT:C12416" + }, { + "val" : "SCTID:302511008" + }, { + "val" : "UMLS:C0041951" + }, { + "val" : "VHOG:0000605" + }, { + "val" : "Wikipedia:Ureter" + }, { + "val" : "XAO:0000144" + }, { + "val" : "galen:Ureter" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000057", + "lbl" : "urethra", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.", + "xrefs" : [ "MGI:anna", "MP:0000537" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "BTO:0001426" + }, { + "val" : "CALOHA:TS-1132" + }, { + "val" : "EFO:0000931" + }, { + "val" : "EMAPA:30901" + }, { + "val" : "EV:0100099" + }, { + "val" : "FMA:19667" + }, { + "val" : "GAID:390" + }, { + "val" : "MA:0000379" + }, { + "val" : "MAT:0000121" + }, { + "val" : "MESH:D014521" + }, { + "val" : "MIAA:0000121" + }, { + "val" : "NCIT:C12417" + }, { + "val" : "SCTID:302513006" + }, { + "val" : "UMLS:C0041967" + }, { + "val" : "VHOG:0001264" + }, { + "val" : "Wikipedia:Urethra" + }, { + "val" : "XAO:0000153" + }, { + "val" : "galen:Urethra" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "lbl" : "duct", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "A tubular structure that transports secreted or excreted substances.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165", "http://www.siumed.edu/~dking2/intro/glands.htm#ducts" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine gland duct" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "ducts", + "xrefs" : [ "XAO:0004000" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011123" + }, { + "val" : "FBbt:00100314" + }, { + "val" : "FMA:30320" + }, { + "val" : "NCIT:C12948" + }, { + "val" : "SCTID:91726008" + }, { + "val" : "TAO:0005171" + }, { + "val" : "UMLS:C0687028" + }, { + "val" : "Wikipedia:Duct_(anatomy)" + }, { + "val" : "XAO:0004000" + }, { + "val" : "ZFA:0005171" + }, { + "val" : "galen:Duct" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000060", + "lbl" : "anatomical wall", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.", + "xrefs" : [ "FMA:82482" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "wall" + }, { + "pred" : "hasExactSynonym", + "val" : "wall of organ", + "xrefs" : [ "FMA:82482" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ wall", + "xrefs" : [ "FMA:82482" ] + } ], + "xrefs" : [ { + "val" : "FMA:82482" + }, { + "val" : "galen:Wall" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. 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See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Located_in" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", - "lbl" : "2D boundary of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000062", + "lbl" : "organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + "val" : "Anatomical structure that performs a specific function or group of functions [WP].", + "xrefs" : [ "Wikipedia:Organ_(anatomy)" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "anatomical unit" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body organ" + }, { + "pred" : "hasRelatedSynonym", + "val" : "element", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:4" + }, { + "val" : "CARO:0020004" + }, { + "val" : "EFO:0000634" + }, { + "val" : "EMAPA:35949" + }, { + "val" : "ENVO:01000162" + }, { + "val" : "FMA:67498" + }, { + "val" : "MA:0003001" + }, { + "val" : "NCIT:C13018" + }, { + "val" : "SCTID:272625005" + }, { + "val" : "UMLS:C0178784" + }, { + "val" : "WBbt:0003760" + }, { + "val" : "Wikipedia:Organ_(anatomy)" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", - "lbl" : "has 2D boundary", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000063", + "lbl" : "organ subunit", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + "val" : "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "organ region with fixed fiat boundary", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ segment", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "segment of organ", + "xrefs" : [ "FMA:86140" ] + } ], + "xrefs" : [ { + "val" : "FMA:86140" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002005", - "lbl" : "innervated_by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002006", - "lbl" : "has synaptic terminal of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002007", - "lbl" : "bounding layer of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000064", + "lbl" : "organ part", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + "val" : "A multicellular structure that is a part of an organ.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cardinal organ part", + "xrefs" : [ "FMA:82472" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "regional part of organ", + "xrefs" : [ "BIRNLEX:16" ] + } ], "xrefs" : [ { - "val" : "RO:0002007" + "val" : "AAO:0011124" + }, { + "val" : "BIRNLEX:16" + }, { + "val" : "EFO:0000635" + }, { + "val" : "FMA:82472" + }, { + "val" : "SCTID:113343008" + }, { + "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bounding_layer_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002021", - "lbl" : "occurs across", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000066", + "lbl" : "fully formed stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + "val" : "The stage of development at which the animal is fully formed, including immaturity and maturity. 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The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO].", + "xrefs" : [ "GO:0001656", "Wikipedia:Metanephros#Metanephros" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "metanephron", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "definite kidney", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "definitive kidney", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "hind kidney", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metanephric kidney", + "xrefs" : [ "VHOG:0000039" ] + } ], + "xrefs" : [ { + "val" : "BTO:0001543" + }, { + "val" : "EHDAA2:0001137" + }, { + "val" : "EHDAA:3089" + }, { + "val" : "EHDAA:5911" + }, { + "val" : "EMAPA:17373" + }, { + "val" : "EMAPA_RETIRED:17207" + }, { + "val" : "FMA:72172" + }, { + "val" : "NCIT:C34209" + }, { + "val" : "SCTID:308797000" + }, { + "val" : "UMLS:C0231049" + }, { + "val" : "VHOG:0000039" + }, { + "val" : "Wikipedia:Metanephros#Metanephros" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO check developmental relationships" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002113", - "lbl" : "has presynaptic terminal in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000083", + "lbl" : "mesonephric tubule", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." + "val" : "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. 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GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "diverticulum", + "xrefs" : [ "BTO:0001646" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "diverticulum metanephricum", + "xrefs" : [ "Wikipedia:Ureteric_bud" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "gemma ureterica", + "xrefs" : [ "Wikipedia:Ureteric_bud" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metanephric bud", + "xrefs" : [ "BTO:0001646" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metanephric diverticulum", + "xrefs" : [ "Wikipedia:Metanephros#Metanephros" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "ureteric ampulla" + }, { + "pred" : "hasRelatedSynonym", + "val" : "ureteric diverticulum", + "xrefs" : [ "VHOG:0000541" ] + } ], + "xrefs" : [ { + "val" : "BTO:0001646" + }, { + "val" : "EHDAA2:0002140" + }, { + "val" : "EHDAA:3091" + }, { + "val" : "EHDAA:5917" + }, { + "val" : "EMAPA:17209" + }, { + "val" : "NCIT:C34207" + }, { + "val" : "SCTID:361528000" + }, { + "val" : "UMLS:C1284058" + }, { + "val" : "VHOG:0000541" + }, { + "val" : "Wikipedia:Ureteric_bud" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that some ( that some Y?)))" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002130", - "lbl" : "has synaptic terminal in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000092", + "lbl" : "post-embryonic stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + "val" : "Stage succeeding embryo, including mature structure.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "postembryonic stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-hatching stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "postembryonic" + } ], + "xrefs" : [ { + "val" : "BilaDO:0000003" + }, { + "val" : "OGES:000010" + }, { + "val" : "OGES:000014" + }, { + "val" : "OGES:000024" + }, { + "val" : "WBls:0000022" + }, { + "val" : "WBls:0000093" + }, { + "val" : "WBls:0000103" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some Y?)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/344" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", - "lbl" : "overlaps", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000104", + "lbl" : "life cycle", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" + "val" : "An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "entire life cycle" + }, { + "pred" : "hasExactSynonym", + "val" : "entire lifespan" + }, { + "pred" : "hasExactSynonym", + "val" : "life" + }, { + "pred" : "hasExactSynonym", + "val" : "lifespan" + } ], "xrefs" : [ { - "val" : "RO:0002131" + "val" : "FBdv:00000000" + }, { + "val" : "HsapDv:0000001" + }, { + "val" : "MmusDv:0000001" + }, { + "val" : "OGES:000011" + }, { + "val" : "ncithesaurus:Life" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/532" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002132", - "lbl" : "has fasciculating neuron projection", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002134", - "lbl" : "innervates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000105", + "lbl" : "life cycle stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." + "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "developmental stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000105" + }, { + "val" : "EFO:0000399" + }, { + "val" : "FBdv:00007012" + }, { + "val" : "FMA:24120" + }, { + "val" : "HsapDv:0000000" + }, { + "val" : "MESH:D008018" + }, { + "val" : "MmusDv:0000000" + }, { + "val" : "OlatDv:0000010" + }, { + "val" : "PdumDv:0000090" + }, { + "val" : "WBls:0000002" + }, { + "val" : "XAO:1000000" + }, { + "val" : "ZFS:0000000" + }, { + "val" : "ZFS:0100000" + }, { + "val" : "ncithesaurus:Developmental_Stage" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that ( some ( that some Y?)))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002150", - "lbl" : "continuous with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000106", + "lbl" : "zygote stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + "val" : "A stage at which the organism is a single cell produced by means of sexual reproduction.", + "xrefs" : [ "Wikipedia:Zygote" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "1-cell stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fertilized egg stage", + "xrefs" : [ "BTO:0000854" ] + }, { + "pred" : "hasExactSynonym", + "val" : "one cell stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fertilized egg stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "one-cell stage", + "xrefs" : [ "VHOG:0000745" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "zygote", + "xrefs" : [ "VHOG:0000745" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "zygotum", + "xrefs" : [ "Wikipedia:Zygote" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000106" + }, { + "val" : "BilaDO:0000005" + }, { + "val" : "EFO:0001322" + }, { + "val" : "EHDAA:27" + }, { + "val" : "FBdv:00005288" + }, { + "val" : "NCIT:C12601" + }, { + "val" : "PdumDv:0000100" + }, { + "val" : "VHOG:0000745" + }, { + "val" : "Wikipedia:Zygote" + }, { + "val" : "XAO:1000001" + }, { + "val" : "ZFS:0000001" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" + "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", - "lbl" : "shares ancestor with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000107", + "lbl" : "cleavage stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + "val" : "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.", + "xrefs" : [ "GO:0040016", "Wikipedia:Cleavage_(embryo)" ] }, - "comments" : [ "VBO calls this homologous_to" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", - "lbl" : "only in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000107" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "val" : "BilaDO:0000006" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." - }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "val" : "EFO:0001290" + }, { + "val" : "FBdv:00000054" + }, { + "val" : "MESH:D002970" + }, { + "val" : "MmusDv:0000004" + }, { + "val" : "OGES:000015" + }, { + "val" : "OGES:000020" + }, { + "val" : "PdumDv:0000200" + }, { + "val" : "Wikipedia:Cleavage_(embryo)" + }, { + "val" : "XAO:1000004" + }, { + "val" : "ZFS:0000046" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000108", + "lbl" : "blastula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000108" + }, { + "val" : "BilaDO:0000007" + }, { + "val" : "EFO:0001282" + }, { + "val" : "HsapDv:0000006" + }, { + "val" : "MmusDv:0000007" + }, { + "val" : "OGES:000003" + }, { + "val" : "OGES:000016" + }, { + "val" : "OGES:000021" + }, { + "val" : "WBls:0000005" + }, { + "val" : "Wikipedia:Blastula" + }, { + "val" : "XAO:1000003" + }, { + "val" : "ZFS:0000045" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "val" : "consider adding a preceding stage 'morula stage' as part of cleavage" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000109", + "lbl" : "gastrula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + "val" : "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.", + "xrefs" : [ "GO:0007369" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blastocystis trilaminaris stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000109" + }, { + "val" : "BilaDO:0000008" + }, { + "val" : "EFO:0001296" + }, { + "val" : "FBdv:00005317" + }, { + "val" : "HsapDv:0000010" + }, { + "val" : "MmusDv:0000013" + }, { + "val" : "OGES:000004" + }, { + "val" : "OGES:000019" + }, { + "val" : "WBls:0000010" + }, { + "val" : "XAO:1000005" + }, { + "val" : "ZFS:0000047" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000110", + "lbl" : "neurula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + "val" : "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.", + "xrefs" : [ "GO:0001841" ] }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "xrefs" : [ { + "val" : "BILS:0000110" + }, { + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000119", + "lbl" : "cell layer", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + "val" : "Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "layer", + "xrefs" : [ "NCIT:C66831" ] + }, { + "pred" : "hasExactSynonym", + "val" : "layer of cells" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cell sheath" + }, { + "pred" : "hasRelatedSynonym", + "val" : "sheath of cells" + } ], + "xrefs" : [ { + "val" : "NCIT:C66831" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + "val" : "consider adding to caro" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000154", + "lbl" : "posterior region of body", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000158", + "lbl" : "membranous layer", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002180" + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "membrane" + }, { + "pred" : "hasExactSynonym", + "val" : "membranous organ component", + "xrefs" : [ "FMA:82500" ] } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + "xrefs" : [ { + "val" : "FMA:30322" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "FMA:82500" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "val" : "MESH:D008566" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "val" : "NCIT:C12749" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000161", + "lbl" : "orifice", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + "val" : "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].", + "xrefs" : [ "FMA:3724" ] }, - "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "anatomical ostium", + "xrefs" : [ "FMA:3724" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "ostium" + }, { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "val" : "anatomical orifice", + "xrefs" : [ "FMA:3724" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "hilum" + } ], "xrefs" : [ { - "val" : "RO:0002211" + "val" : "FMA:3724" + }, { + "val" : "SCTID:91837002" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000162", + "lbl" : "cloaca", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + "val" : "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.", + "xrefs" : [ "ISBN:0073040584", "Wikipedia:Cloaca" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "cloacal chamber", + "xrefs" : [ "AAO:0000095" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vent", + "xrefs" : [ "XAO:0000244" ] + } ], "xrefs" : [ { - "val" : "RO:0002212" + "val" : "AAO:0000095" + }, { + "val" : "GAID:1206" + }, { + "val" : "MESH:D002988" + }, { + "val" : "NCIT:C34127" + }, { + "val" : "SCTID:362857006" + }, { + "val" : "SCTID:370631000" + }, { + "val" : "UMLS:C0008987" + }, { + "val" : "VHOG:0001186" + }, { + "val" : "Wikipedia:Cloaca" + }, { + "val" : "XAO:0000244" + }, { + "val" : "ZFA:0005781" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "negatively_regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000163", + "lbl" : "embryonic cloaca", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + "val" : "Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].", + "xrefs" : [ "MP:0010115", "Wikipedia:Cloaca_(embryology)" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "cloaca" + } ], "xrefs" : [ { - "val" : "RO:0002213" + "val" : "EHDAA2:0000256" + }, { + "val" : "EHDAA:4895" + }, { + "val" : "EMAPA:27573" + }, { + "val" : "Wikipedia:Cloaca_(embryology)" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "positively_regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000164", + "lbl" : "primitive urogenital sinus", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "embryonic tissue", + "xrefs" : [ "FMA:69069" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://en.wikipedia.org/wiki/Tributary" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002379", - "lbl" : "spatially coextensive with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002380", - "lbl" : "branching part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" - 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", + "lbl" : "ectoderm", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", + "xrefs" : [ "Wikipedia:Ectoderm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic ectoderm", + "xrefs" : [ "VHOG:0000153" ] + } ], "xrefs" : [ { - 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Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", - "lbl" : "composed primarily of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000926", + "lbl" : "mesoderm", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + "val" : "The middle germ layer of the embryo, between the endoderm and ectoderm.", + "xrefs" : [ "Wikipedia:Mesoderm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "embryonic mesoderm", + "xrefs" : [ "VHOG:0000152" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "entire mesoderm", + "xrefs" : [ "SCTID:362854004", "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mesodermal mantle" + } ], + "xrefs" : [ { + "val" : "AAO:0000304" + }, { + "val" : "BILA:0000037" + }, { + "val" : "BTO:0000839" + }, { + "val" : "CALOHA:TS-0623" + }, { + "val" : "EFO:0001981" + }, { + "val" : "EHDAA2:0001128" + }, { + "val" : "EHDAA:124" + }, { + "val" : "EHDAA:160" + }, { + "val" : "EHDAA:183" + }, { + "val" : "EMAPA:16083" + }, { + "val" : "EV:0100006" + }, { + "val" : "FBbt:00000126" + }, { + "val" : "FMA:69072" + }, { + "val" : "GAID:522" + }, { + "val" : "MAT:0000174" + }, { + "val" : "MESH:D008648" + }, { + "val" : "MIAA:0000174" + }, { + "val" : "NCIT:C12750" + }, { + "val" : "SCTID:362854004" + }, { + "val" : "TAO:0000041" + }, { + "val" : "UMLS:C0025485" + }, { + "val" : "VHOG:0000152" + }, { + "val" : "Wikipedia:Mesoderm" + }, { + "val" : "XAO:0000050" + }, { + "val" : "ZFA:0000041" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", - "lbl" : "has part that occurs in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000930", + "lbl" : "stomodeum", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + "val" : "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.", + "xrefs" : [ "Wikipedia:Stomodeum", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/326" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "lbl" : "receives input from", - "type" : "PROPERTY", - "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "stomodeal-hypophyseal primordium", + "xrefs" : [ "XAO:0000269" ] + }, { + "pred" : "hasExactSynonym", + "val" : "mouth primordium", + "xrefs" : [ "XAO:0000269" ] + }, { + "pred" : "hasExactSynonym", + "val" : "primitive oral cavity", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "stomatodeum", + "xrefs" : [ "Wikipedia:Stomodeum" ] + }, { + "pred" : "hasExactSynonym", + "val" : "stomodaeum" + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth pit", + "xrefs" : [ "EMAPA:16263" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral ectoderm", + "xrefs" : [ "ZFA:0001290", "ZFIN:ZDB-PUB-100726-23" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral pit", + "xrefs" : [ "EMAPA:16263" ] + } ], + "xrefs" : [ { + "val" : "BTO:0004224" + }, { + "val" : "EHDAA2:0001929" + }, { + "val" : "EMAPA:16263" + }, { + "val" : "FBbt:00000439" + }, { + "val" : "FMA:295846" + }, { + "val" : "NCIT:C34306" + }, { + "val" : "TAO:0001290" + }, { + "val" : "TGMA:0000135" + }, { + "val" : "UMLS:C1514977" + }, { + "val" : "Wikipedia:Stomodeum" + }, { + "val" : "XAO:0000269" + }, { + "val" : "ZFA:0001290" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" + "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "lbl" : "sends output to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000931", + "lbl" : "proctodeum", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.", + "xrefs" : [ "ZFA:0000066", "https://github.com/obophenotype/uberon/issues/685", "https://sourceforge.net/p/fbbtdv/tickets/52" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic proctodaeum" + }, { + "pred" : "hasExactSynonym", + "val" : "proctodaeum" + }, { + "pred" : "hasNarrowSynonym", + "val" : "amnioproctodeal invagination", + "xrefs" : [ "FBbt:00000123" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "anal pit", + "xrefs" : [ "VHOG:0000139" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "anus porus", + "xrefs" : [ "XAO:0001019" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011087" + }, { + "val" : "EHDAA2:0000121" + }, { + "val" : "EMAPA:25038" + }, { + "val" : "FBbt:00000123" + }, { + "val" : "NCIT:C34278" + }, { + "val" : "TAO:0000066" + }, { + "val" : "UMLS:C0231054" + }, { + "val" : "VHOG:0000139" + }, { + "val" : "Wikipedia:Proctodeum" + }, { + "val" : "XAO:0001019" + }, { + "val" : "ZFA:0000066" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "val" : "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/685" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", - "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", - "lbl" : "existence starts during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002489", - "lbl" : "existence starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002490", - "lbl" : "existence overlaps", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002491", - "lbl" : "existence starts and ends during", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000948", + "lbl" : "heart", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + "val" : "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.", + "xrefs" : [ "Wikipedia:Heart", "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "comments" : [ "Taxon notes:\" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)\" DOI:10.1101/gad.1485706" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "exists during" + "val" : "chambered heart", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate heart" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasNarrowSynonym", + "val" : "branchial heart" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardium", + "xrefs" : [ "EMAPA:16105" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010210" + }, { + "val" : "BILA:0000020" + }, { + "val" : "BTO:0000562" + }, { + "val" : "CALOHA:TS-0445" + }, { + "val" : "EFO:0000815" + }, { + "val" : "EHDAA2:0000738" + }, { + "val" : "EHDAA:420" + }, { + "val" : "EMAPA:16105" + }, { + "val" : "EV:0100018" + }, { + "val" : "FMA:7088" + }, { + "val" : "GAID:174" + }, { + "val" : "MA:0000072" + }, { + "val" : "MAT:0000036" + }, { + "val" : "MESH:D006321" + }, { + "val" : "MIAA:0000036" + }, { + "val" : "NCIT:C12727" + }, { + "val" : "SCTID:302509004" + }, { + "val" : "TAO:0000114" + }, { + "val" : "UMLS:C0018787" + }, { + "val" : "VHOG:0000276" + }, { + "val" : "Wikipedia:Heart" + }, { + "val" : "XAO:0000064" + }, { + "val" : "ZFA:0000114" + }, { + "val" : "galen:Heart" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6239" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", - "lbl" : "existence ends during", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000957", + "lbl" : "lamina", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + "val" : "Any thin layer or plate.", + "xrefs" : [ "Wikipedia:Lamina_of_the_vertebral_arch" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "laminar tissue" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Lamina_of_the_vertebral_arch" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - merge with cell layer?" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002493", - "lbl" : "existence ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000958", + "lbl" : "medulla of organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + "val" : "Middle part of an organ, surrounded by the cortex.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", - "lbl" : "transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002495", - "lbl" : "immediate transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - } + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "medulla", + "xrefs" : [ "FMA:61108" ] + } ], + "xrefs" : [ { + "val" : "FMA:61108" + }, { + "val" : "galen:Medulla" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002496", - "lbl" : "existence starts during or after", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000982", + "lbl" : "skeletal joint", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + "val" : "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].", + "xrefs" : [ "GO_REF:0000034", "VSAO:0000101", "Wikipedia:Joint", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", - "lbl" : "existence ends during or before", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "articulation", + "xrefs" : [ "VSAO:0000101" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "joint", + "xrefs" : [ "FMA:7490", "VSAO:0000101" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "articular joint", + "xrefs" : [ "BTO:0001686" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "joints", + "xrefs" : [ "ZFA:0001596" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000182" + }, { + "val" : "BTO:0001686" + }, { + "val" : "CALOHA:TS-2023" + }, { + "val" : "EFO:0000948" + }, { + "val" : "EMAPA:35456" + }, { + "val" : "FMA:7490" + }, { + "val" : "GAID:102" + }, { + "val" : "MA:0000319" + }, { + "val" : "MAT:0000188" + }, { + "val" : "MESH:D007596" + }, { + "val" : "MIAA:0000188" + }, { + "val" : "NCIT:C13044" + }, { + "val" : "RETIRED_EHDAA2:0003182" + }, { + "val" : "SCTID:302536002" + }, { + "val" : "TAO:0000367" + }, { + "val" : "UMLS:C0022417" + }, { + "val" : "VHOG:0001276" + }, { + "val" : "VSAO:0000101" + }, { + "val" : "Wikipedia:Joint" + }, { + "val" : "XAO:0000171" + }, { + "val" : "ZFA:0001596" + }, { + "val" : "galen:Joint" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000990", + "lbl" : "reproductive system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical system that has as its parts the organs concerned with reproduction.", + "xrefs" : [ "Wikipedia:Reproductive_system" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "genital system" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasNarrowSynonym", + "val" : "genitalia" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Geschlechtsorgan", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "animal reproductive system", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "genital tract" + }, { + "pred" : "hasRelatedSynonym", + "val" : "organa genitalia", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "reproductive tissue", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "reproductive tract" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "systemata genitalia", + "xrefs" : [ "Wikipedia:Reproductive_system" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010258" + }, { + "val" : "BILA:0000103" + }, { + "val" : "BTO:0000081" + }, { + "val" : "CALOHA:TS-1318" + }, { + "val" : "EFO:0000809" + }, { + "val" : "EHDAA2:0001603" + }, { + "val" : "EHDAA:5923" + }, { + "val" : "EMAPA:17381" + }, { + "val" : "EV:0100100" + }, { + "val" : "FBbt:00004857" + }, { + "val" : "FMA:7160" + }, { + "val" : "GAID:363" + }, { + "val" : "HAO:0000374" + }, { + "val" : "HAO:0000895" + }, { + "val" : "MA:0000326" + }, { + "val" : "MIAA:0000305" + }, { + "val" : "NCIT:C12841" + }, { + "val" : "SCTID:278875001" + }, { + "val" : "TAO:0000632" + }, { + "val" : "UMLS:C1261210" + }, { + "val" : "VHOG:0000182" + }, { + "val" : "WBbt:0005747" + }, { + "val" : "Wikipedia:Reproductive_system" + }, { + "val" : "XAO:0000142" + }, { + "val" : "ZFA:0000632" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider splitting genitalia from reproductive system" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-06-10T18:22:34Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" + } ] } }, { - 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Examples: vasculature of lung, vasculature of face.", + "xrefs" : [ "ZFA:0005249" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "death" + "pred" : "hasExactSynonym", + "val" : "vascular network", + "xrefs" : [ "FMA:69050" ] } ], "xrefs" : [ { - "val" : "XAO:0000437" + "val" : "BTO:0003718" }, { - "val" : "XtroDO:0000085" + "val" : "FMA:69050" + }, { + "val" : "TAO:0005249" + }, { + "val" : "ZFA:0005249" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "see also: vascular system. 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In metazoans, commences with the zygote stage and ends with the death of the organism.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. 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TODO GCI: relationship: capable_of GO:0030104" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "1-cell stage" - }, { - "pred" : "hasExactSynonym", - "val" : "fertilized egg stage", - "xrefs" : [ "BTO:0000854" ] - }, { - "pred" : "hasExactSynonym", - "val" : "one cell stage" - }, { - "pred" : "hasRelatedSynonym", - "val" : "fertilized egg stage" + "val" : "pronephric kidney", + "xrefs" : [ "XAO:0002000" ] }, { "pred" : "hasRelatedSynonym", - "val" : "one-cell stage", - "xrefs" : [ "VHOG:0000745" ] + "val" : "archinephron", + "xrefs" : [ "BTO:0001541" ] }, { "pred" : "hasRelatedSynonym", - "val" : "zygote", - "xrefs" : [ "VHOG:0000745" ] + "val" : "embryonic kidney", + "xrefs" : [ "BTO:0001541" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "zygotum", - "xrefs" : [ "Wikipedia:Zygote" ] + "val" : "pronephron", + "xrefs" : [ "BTO:0001541" ] } ], "xrefs" : [ { - "val" : "BILS:0000106" + "val" : "AAO:0011089" }, { - "val" : "BilaDO:0000005" + "val" : "BTO:0001541" }, { - "val" : "EFO:0001322" + "val" : "EFO:0000927" }, { - "val" : "EHDAA:27" + "val" : "EHDAA2:0001570" }, { - "val" : "FBdv:00005288" + "val" : "EHDAA:1017" }, { - "val" : "NCIT:C12601" + "val" : "EMAPA:16579" }, { - "val" : "PdumDv:0000100" + "val" : "FMA:72170" }, { - "val" : "VHOG:0000745" + "val" : "MAT:0000117" }, { - "val" : "Wikipedia:Zygote" + "val" : "MIAA:0000117" }, { - "val" : "XAO:1000001" + "val" : "NCIT:C34280" }, { - "val" : "ZFS:0000001" + "val" : "SCTID:308804007" + }, { + "val" : "TAO:0000151" + }, { + "val" : "UMLS:C0231048" + }, { + "val" : "VHOG:0000037" + }, { + "val" : "Wikipedia:Pronephros" + }, { + "val" : "XAO:0002000" + }, { + "val" : "ZFA:0000151" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0005794" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000107", - "lbl" : "cleavage stage", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002193", + "lbl" : "hemolymphoid system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. 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It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. 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The blastula follows the morula and precedes the gastrula in the developmental sequence.", - "xrefs" : [ "Wikipedia:Blastula" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blastula embryo", - "xrefs" : [ "BILA:0000059" ] + "pred" : "hasRelatedSynonym", + "val" : "presumptive central nervous system" }, { "pred" : "hasRelatedSynonym", - "val" : "blastosphere", - "xrefs" : [ "Wikipedia:Blastula" ] + "val" : "ventral neurogenic region", + "xrefs" : [ "VHOG:0000150" ] } ], "xrefs" : [ { - "val" : "BILA:0000059" + "val" : "AAO:0011074" }, { - "val" : "BTO:0000128" + "val" : "BILA:0000039" }, { - "val" : "GAID:1294" + "val" : "CALOHA:TS-1212" }, { - "val" : "MESH:D036703" + "val" : "EHDAA2:0001248" }, { - "val" : "OGEM:000006" + "val" : "EHDAA:1498" }, { - "val" : "Wikipedia:Blastula" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" + "val" : "EHDAA:255" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" + "val" : "EMAPA:16073" + }, { + "val" : "EV:0100004" + }, { + "val" : "FBbt:00001057" + }, { + "val" : "FMA:87657" + }, { + "val" : "MAT:0000176" + }, { + "val" : "MIAA:0000176" + }, { + "val" : "NCIT:C34228" + }, { + "val" : "TAO:0001120" + }, { + "val" : "UMLS:C1518271" + }, { + "val" : "VHOG:0000150" }, { + "val" : "Wikipedia:Neuroectoderm" + }, { + "val" : "XAO:0000042" + }, { + "val" : "ZFA:0001120" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000353", - "lbl" : "parenchyma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002355", + "lbl" : "pelvic region of trunk", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.", - "xrefs" : [ "Wikipedia:Parenchyma" ] + "val" : "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.", + "xrefs" : [ "Wikipedia:Pelvis", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/720" ] }, - "xrefs" : [ { - "val" : "EHDAA:3015" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "lesser pelvis", + "xrefs" : [ "FMA:9578" ] }, { - "val" : "EHDAA:3905" + "pred" : "hasExactSynonym", + "val" : "pelvic region" }, { - "val" : "EHDAA:3999" + "pred" : "hasExactSynonym", + "val" : "pelvis", + "xrefs" : [ "FMA:9578", "MA:0000030" ] }, { - "val" : "EHDAA:4005" + "pred" : "hasExactSynonym", + "val" : "pelvis region" }, { - "val" : "EHDAA:6899" + "pred" : "hasExactSynonym", + "val" : "true pelvis", + "xrefs" : [ "FMA:9578" ] + } ], + "xrefs" : [ { + "val" : "BTO:0001006" }, { - "val" : "EHDAA:6903" + "val" : "CALOHA:TS-2227" }, { - "val" : "EHDAA:6994" + "val" : "EFO:0002805" }, { - "val" : "EHDAA:8086" + "val" : "EMAPA:35931" }, { - "val" : "EHDAA:9182" + "val" : "EV:0100012" }, { - "val" : "EHDAA:9190" + "val" : "FMA:9578" }, { - "val" : "EHDAA:9196" + "val" : "GAID:87" }, { - "val" : "EHDAA:9202" + "val" : "MA:0000030" }, { - "val" : "FMA:45732" + "val" : "MESH:D010388" }, { - "val" : "NCIT:C74601" + "val" : "NCIT:C12767" }, { - "val" : "UMLS:C0933845" + "val" : "SCTID:229765004" }, { - "val" : "Wikipedia:Parenchyma" + "val" : "UMLS:C0030797" + }, { + "val" : "Wikipedia:Pelvis" + }, { + "val" : "galen:Pelvis" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18793,86 +20795,65 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000362", - "lbl" : "renal medulla", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", + "lbl" : "connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The inner portion of the kidney consisting of the renal pyramids.", - "xrefs" : [ "ISBN:0-683-40008-8", "MGI:smb", "MP:0003014" ] + "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] }, - "comments" : [ "Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "kidney medulla", - "xrefs" : [ "OBOL:automatic" ] + "val" : "portion of connective tissue", + "xrefs" : [ "FMA:9640" ] }, { "pred" : "hasExactSynonym", - "val" : "medulla of kidney", - "xrefs" : [ "OBOL:automatic" ] + "val" : "textus connectivus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "medulla renalis", - "xrefs" : [ "FMA:74268", "FMA:TA" ] + "pred" : "hasRelatedSynonym", + "val" : "Bindegewebe", + "xrefs" : [ "BTO:0000421" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000098" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "pyramides renales", - "xrefs" : [ "FMA:74268", "FMA:TA" ] + "val" : "BTO:0000421" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal medullae", - "xrefs" : [ "FMA:86327" ] + "val" : "CALOHA:TS-2009" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal medullae set", - "xrefs" : [ "FMA:86327" ] + "val" : "EFO:0000952" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal pyramids", - "xrefs" : [ "FMA:74268" ] + "val" : "EMAPA:35251" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal pyramids set", - "xrefs" : [ "FMA:74268" ] + "val" : "FMA:9640" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "medullary pyramids", - "xrefs" : [ "FMA:74268" ] + "val" : "GAID:100" }, { - "pred" : "hasRelatedSynonym", - "val" : "renal marrow", - "xrefs" : [ "BTO:0001167" ] - } ], - "xrefs" : [ { - "val" : "BTO:0001167" + "val" : "MA:0000011" }, { - "val" : "CALOHA:TS-1157" + "val" : "MAT:0000301" }, { - "val" : "EMAPA:19279" + "val" : "MESH:D003238" }, { - "val" : "GAID:425" + "val" : "MIAA:0000301" }, { - "val" : "MA:0000373" + "val" : "NCIT:C12374" }, { - "val" : "MESH:D007679" + "val" : "SCTID:361919005" }, { - "val" : "NCIT:C12740" + "val" : "TAO:0001641" }, { - "val" : "SCTID:30737000" + "val" : "UMLS:C0009780" }, { - "val" : "UMLS:C0022664" + "val" : "VSAO:0000017" }, { - "val" : "Wikipedia:Renal_medulla" + "val" : "XAO:0001017" }, { - "val" : "galen:MedullaOfKidney" + "val" : "ZFA:0001632" + }, { + "val" : "galen:ConnectiveTissue" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -18880,1173 +20861,1101 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "lbl" : "musculature of body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", + "lbl" : "muscle tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", - "xrefs" : [ "VSAO:0000033" ] + "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", + "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "pred" : "hasExactSynonym", - "val" : "muscle system" - }, { - "pred" : "hasExactSynonym", - "val" : "muscle system of body" - }, { - "pred" : "hasExactSynonym", - "val" : "muscular system", - "xrefs" : [ "FMA:72954" ] - }, { - "pred" : "hasExactSynonym", - "val" : "musculature system", - "xrefs" : [ "BILA:0000088" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all muscles", - "xrefs" : [ "FMA:72954" ] + "val" : "muscular tissue" }, { "pred" : "hasExactSynonym", - "val" : "set of muscles of body", - "xrefs" : [ "FMA:72954" ] + "val" : "portion of muscle tissue", + "xrefs" : [ "FMA:9641" ] }, { "pred" : "hasExactSynonym", - "val" : "vertebrate muscular system", - "xrefs" : [ "BTO:0001369" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "muskelsystem", - "xrefs" : [ "BTO:0001485" ] + "val" : "textus muscularis" } ], "xrefs" : [ { - "val" : "AAO:0000307" - }, { - "val" : "BILA:0000088" + "val" : "AAO:0000306" }, { - "val" : "BTO:0001369" + "val" : "AEO:0000122" }, { - "val" : "BTO:0001485" + "val" : "CALOHA:TS-0642" }, { - "val" : "EFO:0000801" + "val" : "EHDAA2:0003122" }, { - "val" : "FMA:72954" + "val" : "EMAPA:32715" }, { - "val" : "MA:0002888" + "val" : "FMA:9641" }, { - "val" : "MAT:0000025" + "val" : "MA:0002437" }, { - "val" : "MIAA:0000025" + "val" : "MESH:D009132" }, { - "val" : "VSAO:0000033" + "val" : "NCIT:C12435" }, { - "val" : "XAO:0004042" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" + "val" : "SCTID:91727004" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "val" : "UMLS:C2328219" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "Wikipedia:Muscle_tissue" }, { + "val" : "galen:MuscleTissue" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", + "lbl" : "hematopoietic system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Anatomical system that is involved in the production of hematopoietic cells.", + "xrefs" : [ "Wikipedia:Haematopoiesis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "body fluid or substance", - "xrefs" : [ "MA:0002450" ] + "val" : "haematological system" }, { "pred" : "hasExactSynonym", - "val" : "body substance", - "xrefs" : [ "FMA:9669" ] + "val" : "haemopoietic system" }, { "pred" : "hasExactSynonym", - "val" : "organism substance", - "xrefs" : [ "CARO:0000004" ] + "val" : "organa haemopoietica" }, { - "pred" : "hasExactSynonym", - "val" : "portion of body substance", - "xrefs" : [ "FMA:9669" ] + "pred" : "hasRelatedSynonym", + "val" : "Blutbildungssystem", + "xrefs" : [ "BTO:0000570" ] }, { - "pred" : "hasExactSynonym", - "val" : "portion of organism substance", - "xrefs" : [ "ZFA:0001487" ] + "pred" : "hasRelatedSynonym", + "val" : "haematopoietic system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hematological system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hematolymphoid system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hemopoietic system" } ], "xrefs" : [ { - "val" : "AAO:0010839" + "val" : "AAO:0011002" + }, { + "val" : "BTO:0000570" }, { - "val" : "AEO:0000004" + "val" : "CALOHA:TS-0449" }, { - "val" : "BILA:0000004" + "val" : "EFO:0000798" }, { - "val" : "CALOHA:TS-2101" + "val" : "EMAPA:35402" }, { - "val" : "CARO:0000004" + "val" : "EV:0100045" }, { - "val" : "EHDAA2:0003004" + "val" : "FMA:9667" }, { - "val" : "EMAPA:35178" + "val" : "GAID:1008" }, { - "val" : "FBbt:00007019" + "val" : "MA:0002434" }, { - "val" : "FMA:9669" + "val" : "MAT:0000022" }, { - "val" : "HAO:0000004" + "val" : "MESH:D006413" }, { - "val" : "MA:0002450" + "val" : "MIAA:0000022" }, { - "val" : "NCIT:C13236" + "val" : "NCIT:C12909" }, { - "val" : "SPD:0000008" + "val" : "SCTID:362587009" }, { - "val" : "TAO:0001487" + "val" : "TAO:0005023" }, { - "val" : "TGMA:0001824" + "val" : "UMLS:C0018957" }, { - "val" : "VHOG:0001726" + "val" : "VHOG:0001624" }, { - "val" : "XAO:0004001" + "val" : "Wikipedia:Haematopoiesis" }, { - "val" : "ZFA:0001487" + "val" : "XAO:0000122" }, { - "val" : "galen:BodySubstance" + "val" : "ZFA:0005023" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000464", - "lbl" : "anatomical space", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002417", + "lbl" : "abdominal segment of trunk", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "The abdominal segment of the torso.", + "xrefs" : [ "Wikipedia:Lumbar" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lumen" + "pred" : "hasRelatedSynonym", + "val" : "abdomen/pelvis/perineum", + "xrefs" : [ "MA:0000021" ] }, { - "pred" : "hasBroadSynonym", - "val" : "space" + "pred" : "hasRelatedSynonym", + "val" : "lower body", + "xrefs" : [ "MA:0000021" ] }, { - "pred" : "hasExactSynonym", - "val" : "lumen space" + "pred" : "hasRelatedSynonym", + "val" : "lower trunk", + "xrefs" : [ "FMA:259211" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "anatomical spaces", - "xrefs" : [ "ZFA:0001643" ] + "val" : "lumbar region", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { - "val" : "AAO:0010110" - }, { - "val" : "AEO:0000005" - }, { - "val" : "BILA:0000005" - }, { - "val" : "CARO:0000005" - }, { - "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" - }, { - "val" : "FMA:5897" - }, { - "val" : "HAO:0000005" - }, { - "val" : "NCIT:C94478" - }, { - "val" : "TAO:0001668" - }, { - "val" : "TGMA:0001825" + "val" : "EMAPA:35104" }, { - "val" : "UMLS:C0524461" + "val" : "FMA:259211" }, { - "val" : "VHOG:0001728" + "val" : "MA:0000021" }, { - "val" : "XAO:0003190" + "val" : "SCTID:362875007" }, { - "val" : "ZFA:0001643" + "val" : "Wikipedia:Lumbar" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", + "lbl" : "epiblast (generic)", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has mass.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", + "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "AAO:0010264" - }, { - "val" : "AEO:0000006" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "epiblast", + "xrefs" : [ "VHOG:0000243" ] }, { - "val" : "BILA:0000006" + "pred" : "hasRelatedSynonym", + "val" : "blastocyst" }, { - "val" : "CARO:0000006" + "pred" : "hasRelatedSynonym", + "val" : "ectoblast", + "xrefs" : [ "MP:0003886" ] }, { - "val" : "EHDAA2:0003006" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "epiblastus", + "xrefs" : [ "Wikipedia:Epiblast" ] }, { - "val" : "FBbt:00007016" + "pred" : "hasRelatedSynonym", + "val" : "primitive ectoderm", + "xrefs" : [ "VHOG:0000243" ] + } ], + "xrefs" : [ { + "val" : "BTO:0004593" }, { - "val" : "FMA:67165" + "val" : "FMA:296704" }, { - "val" : "HAO:0000006" + "val" : "MAT:0000067" }, { - "val" : "TAO:0001836" + "val" : "MIAA:0000067" }, { - "val" : "TGMA:0001826" + "val" : "VHOG:0000243" }, { - "val" : "VHOG:0001721" + "val" : "Wikipedia:Epiblast" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. 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Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", + "xrefs" : [ "FMA:67552" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "immaterial physical anatomical entity", - "xrefs" : [ "FMA:67112" ] + "pred" : "hasBroadSynonym", + "val" : "cavity" } ], "xrefs" : [ { - "val" : "AAO:0010265" - }, { - "val" : "AEO:0000007" - }, { - "val" : "BILA:0000007" - }, { - "val" : "CARO:0000007" - }, { - "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" + "val" : "BIRNLEX:1011" }, { - "val" : "FMA:67112" + "val" : "EMAPA:37442" }, { - "val" : "HAO:0000007" + "val" : "FMA:67552" }, { - "val" : "TAO:0001835" + "val" : "MA:0002447" }, { - "val" : "TGMA:0001827" + "val" : "NCIT:C34007" }, { - 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Examples: pulmonary alveolar epithelium, endothelium.[FMA].", - "xrefs" : [ "FMA:45565", "Wikipedia:Simple_squamous_epithelium", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "An organ involved in reproduction.", + "xrefs" : [ "UBERON:xp" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "epithelium simplex squamosum" + "val" : "genital organ" + }, { + "pred" : "hasExactSynonym", + "val" : "reproductive system organ" + }, { + "pred" : "hasExactSynonym", + "val" : "sex organ" }, { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "simple squamous epithelia", - "xrefs" : [ "ZFA:0001498" ] + "val" : "genitalia" } ], "xrefs" : [ { - "val" : "AAO:0010066" - }, { - "val" : "AEO:0000070" - }, { - "val" : "BILA:0000070" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000070" - }, { - "val" : "EHDAA2:0003070" - }, { - "val" : "FMA:45565" + "val" : "EMAPA:37731" }, { - "val" : "HAO:0000070" + "val" : "MA:0001752" }, { - "val" : "NCIT:C13178" + "val" : "MESH:D005835" }, { - "val" : "TAO:0001498" + "val" : "NCIT:C25177" }, { - "val" : "UMLS:C0836133" + "val" : "SCTID:128181006" }, { - "val" : "Wikipedia:Simple_squamous_epithelium" + "val" : "TGMA:0000591" }, { - "val" : "XAO:0004010" + "val" : "UMLS:C0017420" }, { - "val" : "ZFA:0001498" + "val" : "WBbt:0008422" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000489", - "lbl" : "cavitated compound organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003220", + "lbl" : "metanephric mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Compound organ that contains one or more macroscopic anatomical spaces.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].", + "xrefs" : [ "GO:0072075", "Wikipedia:Metanephric_blastema" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "comments" : [ "Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 \"Developmental Biology\"]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "cavitated organ", - "xrefs" : [ "FMA:55671" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "cavitated compound organs", - "xrefs" : [ "ZFA:0001490" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010016" - }, { - "val" : "AEO:0000072" + "val" : "metanephric blastema", + "xrefs" : [ "Wikipedia:Metanephric_blastema" ] }, { - "val" : "BILA:0000072" + "pred" : "hasExactSynonym", + "val" : "metanephric mesoderm", + "xrefs" : [ "Wikipedia:Metanephric_blastema" ] }, { - "val" : "CARO:0000072" + "pred" : "hasExactSynonym", + "val" : "metanephrogenic mesenchyme", + "xrefs" : [ "EHDAA:5021" ] }, { - "val" : "EHDAA2:0003072" + "pred" : "hasExactSynonym", + "val" : "metanephros associated mesenchyme", + "xrefs" : [ "RETIRED_EHDAA2:0001139" ] + } ], + "xrefs" : [ { + "val" : "EHDAA2:0004062" }, { - "val" : "FMA:55671" + "val" : "EHDAA:4041" }, { - "val" : "HAO:0000072" + "val" : "EHDAA:5021" }, { - "val" : "TAO:0001490" + "val" : "EHDAA:5915" }, { - "val" : "TGMA:0001857" + "val" : "EMAPA:17375" }, { - "val" : "VHOG:0001730" + "val" : "SCTID:361529008" }, { - "val" : "XAO:0003165" + "val" : "VHOG:0000540" }, { - "val" : "ZFA:0001490" + "val" : "Wikipedia:Metanephric_blastema" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -20054,97 +21963,98 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000490", - "lbl" : "unilaminar epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003479", + "lbl" : "thoracic cavity vein", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].", - "xrefs" : [ "FMA:45561", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "A vein that is part of a thoracic cavity [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "simple epithelium", - "xrefs" : [ "FMA:45561" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "unilaminar epithelia", - "xrefs" : [ "ZFA:0001495" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010062" - }, { - "val" : "AEO:0000073" - }, { - "val" : "BILA:0000073" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000073" + "val" : "cavity of chest vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "EHDAA2:0003073" + "pred" : "hasExactSynonym", + "val" : "cavity of thorax vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "FMA:45561" + "pred" : "hasExactSynonym", + "val" : "chest cavity vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "HAO:0000073" + "pred" : "hasExactSynonym", + "val" : "pectoral cavity vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "NCIT:C33554" + "pred" : "hasExactSynonym", + "val" : "vein of cavity of chest", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "SCTID:309043004" + "pred" : "hasExactSynonym", + "val" : "vein of cavity of thorax", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "TAO:0001495" + "pred" : "hasExactSynonym", + "val" : "vein of chest cavity", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "UMLS:C0682574" + "pred" : "hasExactSynonym", + "val" : "vein of pectoral cavity", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "XAO:0004007" + "pred" : "hasExactSynonym", + "val" : "vein of thoracic cavity", + "xrefs" : [ "OBOL:automatic" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37242" }, { - "val" : "ZFA:0001495" + "val" : "MA:0001903" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000915", - "lbl" : "thoracic segment of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003497", + "lbl" : "abdomen blood vessel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Subdivision of trunk that lies between the head and the abdomen.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A blood vessel that is part of an abdomen [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "thorax", - "xrefs" : [ "MA:0000022" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "anterior subdivision of trunk" - }, { - "pred" : "hasRelatedSynonym", - "val" : "upper body" - }, { - "pred" : "hasRelatedSynonym", - "val" : "upper trunk", - "xrefs" : [ "FMA:259209" ] + "val" : "blood vessel of abdomen", + "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "EMAPA:35862" - }, { - "val" : "FMA:259209" - }, { - "val" : "MA:0000022" - }, { - "val" : "SCTID:302551006" + "val" : "MA:0000518" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0003509", + "lbl" : "arterial blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "only in MA - supertype of artery, arteriole, aorta." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "EMAPA:35144" }, { - "val" : "Wikipedia:Thorax" + "val" : "MA:0000061" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -20152,220 +22062,246 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000916", - "lbl" : "abdomen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003513", + "lbl" : "trunk blood vessel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A blood vessel that is part of a trunk [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "abdominopelvic region", - "xrefs" : [ "FMA:9577" ] + "val" : "blood vessel of torso", + "xrefs" : [ "OBOL:automatic" ] }, { "pred" : "hasExactSynonym", - "val" : "abdominopelvis", - "xrefs" : [ "FMA:9577" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "adult abdomen" - }, { - "pred" : "hasRelatedSynonym", - "val" : "belly" + "val" : "blood vessel of trunk", + "xrefs" : [ "OBOL:automatic" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "celiac region" + "pred" : "hasExactSynonym", + "val" : "torso blood vessel", + "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "BTO:0000020" - }, { - "val" : "CALOHA:TS-0001" - }, { - "val" : "EFO:0000968" - }, { - "val" : "EMAPA:35102" - }, { - "val" : "EV:0100011" - }, { - "val" : "FMA:9577" - }, { - "val" : "GAID:16" - }, { - "val" : "MA:0000029" - }, { - "val" : "MAT:0000298" - }, { - "val" : "MESH:D000005" - }, { - "val" : "MIAA:0000298" - }, { - "val" : "SCTID:302553009" - }, { - "val" : "Wikipedia:Abdomen" + "val" : "EMAPA:37237" }, { - "val" : "galen:Abdomen" + "val" : "MA:0000511" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Vertebrate specific. 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"id" : "http://purl.obolibrary.org/obo/UBERON_0000982", - "lbl" : "skeletal joint", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004122", + "lbl" : "genitourinary system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].", - "xrefs" : [ "GO_REF:0000034", "VSAO:0000101", "Wikipedia:Joint", "http://dx.plos.org/10.1371/journal.pone.0051070" ] + "val" : "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.", + "xrefs" : [ "VHOG:0000286" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "articulation", - "xrefs" : [ "VSAO:0000101" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "joint", - "xrefs" : [ "FMA:7490", "VSAO:0000101" ] + "pred" : "hasExactSynonym", + "val" : "urogenital system" }, { "pred" : "hasRelatedSynonym", - "val" : "articular joint", - "xrefs" : [ "BTO:0001686" ] + "val" : "GU tract" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "joints", - "xrefs" : [ "ZFA:0001596" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000182" - }, { - "val" : "BTO:0001686" - }, { - "val" : "CALOHA:TS-2023" + "val" : "UG tract" }, { - "val" : "EFO:0000948" + "pred" : "hasRelatedSynonym", + "val" : "Urogenitalsystem", + "xrefs" : [ "BTO:0003091" ] }, { - "val" : "EMAPA:35456" + "pred" : "hasRelatedSynonym", + "val" : "genito-urinary system", + "xrefs" : [ "FMA:280610" ] }, { - "val" : "FMA:7490" + "pred" : "hasRelatedSynonym", + "val" : "genitourinary tract" }, { - "val" : "GAID:102" + "pred" : "hasRelatedSynonym", + "val" : "urogenital tract", + "xrefs" : [ "BTO:0003091" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000624" }, { - "val" : "MA:0000319" + "val" : "BILA:0000122" }, { - "val" : "MAT:0000188" + "val" : "BTO:0003091" }, { - "val" : "MESH:D007596" + "val" : "EFO:0003864" }, { - "val" : "MIAA:0000188" + "val" : "EHDAA:1013" }, { - "val" : "NCIT:C13044" + "val" : "EMAPA:16367" }, { - "val" : "RETIRED_EHDAA2:0003182" + "val" : "EV:0100094" }, { - "val" : "SCTID:302536002" + "val" : "FMA:280610" }, { - "val" : "TAO:0000367" + "val" : "GAID:362" }, { - "val" : "UMLS:C0022417" + "val" : "MESH:D014566" }, { - "val" : "VHOG:0001276" + "val" : "NCIT:C12810" }, { - "val" : "VSAO:0000101" + "val" : "SCTID:278861008" }, { - "val" : "Wikipedia:Joint" + "val" : "UMLS:C0042066" }, { - "val" : "XAO:0000171" + "val" : "VHOG:0000286" }, { - "val" : "ZFA:0001596" + "val" : "XAO:0000140" }, { - "val" : "galen:Joint" + "val" : "galen:GenitoUrinarySystem" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -20973,665 +22722,370 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000990", - "lbl" : "reproductive system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004134", + "lbl" : "proximal tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that has as its parts the organs concerned with reproduction.", - "xrefs" : [ "Wikipedia:Reproductive_system" ] + "val" : "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].", + "xrefs" : [ "GO:0072014" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "genital system" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasNarrowSynonym", - "val" : "genitalia" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Geschlechtsorgan", - "xrefs" : [ "BTO:0000081" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "animal reproductive system", - "xrefs" : [ "BTO:0000081" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "genital tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "organa genitalia", - "xrefs" : [ "BTO:0000081" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "reproductive tissue", - "xrefs" : [ "BTO:0000081" ] + "pred" : "hasExactSynonym", + "val" : "kidney proximal tubule", + "xrefs" : [ "MA:0002611" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "reproductive tract" + "pred" : "hasExactSynonym", + "val" : "proximal kidney tubule", + "xrefs" : [ "MESH:A05.810.453.736.560.570" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "systemata genitalia", - "xrefs" : [ "Wikipedia:Reproductive_system" ] + "pred" : "hasExactSynonym", + "val" : "renal proximal tubule" } ], "xrefs" : [ { - "val" : "AAO:0010258" - }, { - "val" : "BILA:0000103" - }, { - "val" : "BTO:0000081" - }, { - "val" : "CALOHA:TS-1318" - }, { - "val" : "EFO:0000809" - }, { - "val" : "EHDAA2:0001603" - }, { - "val" : "EHDAA:5923" - }, { - "val" : "EMAPA:17381" - }, { - "val" : "EV:0100100" - }, { - "val" : "FBbt:00004857" - }, { - "val" : "FMA:7160" - }, { - "val" : "GAID:363" - }, { - "val" : "HAO:0000374" - }, { - "val" : "HAO:0000895" - }, { - "val" : "MA:0000326" - }, { - "val" : "MIAA:0000305" - }, { - "val" : "NCIT:C12841" - }, { - "val" : "SCTID:278875001" - }, { - "val" : "TAO:0000632" - }, { - "val" : "UMLS:C1261210" - }, { - "val" : "VHOG:0000182" + "val" : "BTO:0001498" }, { - "val" : "WBbt:0005747" + "val" : "CALOHA:TS-0509" }, { - "val" : "Wikipedia:Reproductive_system" + "val" : "EMAPA:28281" }, { - "val" : "XAO:0000142" + "val" : "MA:0002611" }, { - "val" : "ZFA:0000632" + "val" : "MESH:D007687" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider splitting genitalia from reproductive system" + "val" : "TODO - ensure definition works across species." }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2022-06-10T18:22:34Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000991", - "lbl" : "gonad", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004135", + "lbl" : "distal tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Reproductive organ that produces and releases eggs (ovary) or sperm (testis).", - "xrefs" : [ "ISBN:0140512888", "Wikipedia:Gonad", "ZFA:0000413", "ZFIN:curator" ] + "val" : "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments.", + "xrefs" : [ "GO:0072017" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "gonada" + "val" : "kidney distal tubule", + "xrefs" : [ "MA:0002633" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "gonads", - "xrefs" : [ "ZFA:0000413" ] + "pred" : "hasExactSynonym", + "val" : "renal distal tubule" } ], "xrefs" : [ { - "val" : "AAO:0000213" - }, { - "val" : "BILA:0000123" - }, { - "val" : "BSA:0000079" - }, { - "val" : "BTO:0000534" - }, { - "val" : "EMAPA:17383" - }, { - "val" : "FMA:18250" - }, { - "val" : "GAID:368" - }, { - "val" : "HAO:0000379" - }, { - "val" : "MA:0002420" - }, { - "val" : "MESH:D006066" - }, { - "val" : "NCIT:C12725" - }, { - "val" : "SCTID:304623008" - }, { - "val" : "TAO:0000413" - }, { - "val" : "UMLS:C0018067" + "val" : "BTO:0000482" }, { - "val" : "VHOG:0000397" + "val" : "CALOHA:TS-0504" }, { - "val" : "WBbt:0005175" + "val" : "EMAPA:28387" }, { - "val" : "Wikipedia:Gonad" + "val" : "MA:0002633" }, { - "val" : "XAO:0003146" + "val" : "MESH:D007686" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004136", + "lbl" : "intermediate tubule", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules.", + "xrefs" : [ "GO:0072018" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "renal intermediate tubule" }, { - "val" : "ZFA:0000413" + "pred" : "hasExactSynonym", + "val" : "tubulus attenuatus", + "xrefs" : [ "FMA:17718" ] + } ], + "xrefs" : [ { + "val" : "FMA:17718" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check for applicability across species" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001007", - "lbl" : "digestive system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", + "lbl" : "cardiogenic plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.", - "xrefs" : [ "FB:gg", "NLM:alimentary+system", "Wikipedia:Digestive_system" ] + "val" : "The first recognizable structure derived from the heart field.", + "xrefs" : [ "GO:0003142" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system" + "pred" : "hasExactSynonym", + "val" : "myocardial plate", + "xrefs" : [ "EHDAA2:0000215" ] }, { "pred" : "hasRelatedSynonym", - "val" : "alimentary tract" + "val" : "cardiac crescent", + "xrefs" : [ "EMAPA:16106" ] }, { "pred" : "hasRelatedSynonym", - "val" : "gastrointestinal system" + "val" : "cardiogenic crescent", + "xrefs" : [ "GO:0003142" ] }, { "pred" : "hasRelatedSynonym", - "val" : "gut" + "val" : "heart rudiment" } ], "xrefs" : [ { - "val" : "AAO:0000129" - }, { - "val" : "BILA:0000082" - }, { - "val" : "BTO:0000058" - }, { - "val" : "CALOHA:TS-1293" - }, { - "val" : "EFO:0000793" - }, { - "val" : "FBbt:00005055" - }, { - "val" : "FMA:7152" - }, { - "val" : "GAID:278" - }, { - "val" : "MA:0002431" - }, { - "val" : "MAT:0000018" - }, { - "val" : "MESH:D004064" - }, { - "val" : "MIAA:0000018" - }, { - "val" : "SCTID:278859004" - }, { - "val" : "TADS:0000170" - }, { - "val" : "TAO:0000339" - }, { - "val" : "WBbt:0005748" - }, { - "val" : "Wikipedia:Digestive_system" - }, { - "val" : "XAO:0000125" - }, { - "val" : "ZFA:0000339" + "val" : "EHDAA2:0000215" }, { - "val" : "galen:DigestiveSystem" + "val" : "EMAPA:16106" }, { - "val" : "ncithesaurus:Digestive_System" + "val" : "VHOG:0000975" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001008", - "lbl" : "renal system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "lbl" : "primary heart field", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.", - "xrefs" : [ "DOI:10.1371/journal.pone.0099864", "GO:0072001" ] + "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", + "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] }, - "comments" : [ "EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "excretory system" - }, { - "pred" : "hasExactSynonym", - "val" : "systema urinaria", - "xrefs" : [ "FMA:7159" ] - }, { "pred" : "hasExactSynonym", - "val" : "systema urinarium", - "xrefs" : [ "BTO:0003092" ] + "val" : "first heart field", + "xrefs" : [ "XAO:0004185" ] }, { "pred" : "hasExactSynonym", - "val" : "urinary system" + "val" : "primary heart field", + "xrefs" : [ "PMID:17276708", "XAO:0004185" ] }, { - "pred" : "hasExactSynonym", - "val" : "urinary tract" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "FHF", + "xrefs" : [ "XAO:0004185" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", - "val" : "renal or urinary system", - "xrefs" : [ "EHDAA:5901" ] + "val" : "PHF", + "xrefs" : [ "XAO:0004185" ] }, { "pred" : "hasRelatedSynonym", - "val" : "renal/urinary system" + "val" : "heart field", + "xrefs" : [ "XAO:0004185" ] } ], "xrefs" : [ { - "val" : "AAO:0010257" - }, { - "val" : "BILA:0000015" - }, { - "val" : "BTO:0001244" - }, { - "val" : "BTO:0003092" - }, { - "val" : "CALOHA:TS-1323" - }, { - "val" : "EFO:0000803" - }, { - "val" : "EHDAA2:0001601" - }, { - "val" : "EHDAA:5901" - }, { - "val" : "EMAPA:17366" - }, { - "val" : "EV:0100095" - }, { - "val" : "FBbt:00005056" - }, { - "val" : "FMA:7159" - }, { - "val" : "GAID:391" - }, { - "val" : "MA:0000325" - }, { - "val" : "MAT:0000027" - }, { - "val" : "MESH:D014551" - }, { - "val" : "MIAA:0000027" - }, { - "val" : "NCIT:C12413" - }, { - "val" : "SCTID:362204003" - }, { - "val" : "TADS:0000162" + "val" : "XAO:0004185" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", + "lbl" : "heart tube", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelial tube that will give rise to the mature heart.", + "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic heart tube", + "xrefs" : [ "GO:0003143" ] }, { - "val" : "TAO:0000163" + "pred" : "hasExactSynonym", + "val" : "endocardial heart tube", + "xrefs" : [ "MP:0012700" ] }, { - "val" : "UMLS:C1508753" + "pred" : "hasExactSynonym", + "val" : "endocardial tube", + "xrefs" : [ "XAO:0000337" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010411" }, { - "val" : "VHOG:0000723" + "val" : "EFO:0003526" }, { - "val" : "WBbt:0005736" + "val" : "EMAPA:32685" }, { - "val" : "Wikipedia:Excretory_system" + "val" : "NCIT:C34161" }, { - "val" : "XAO:0000143" + "val" : "TAO:0000360" }, { - "val" : "ZFA:0000163" + "val" : "XAO:0000337" }, { - "val" : "galen:UrinaryTract" + "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "lbl" : "circulatory system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "lbl" : "cardiac chamber", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", - "xrefs" : [ "Wikipedia:Circulatory_system" ] + "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", + "xrefs" : [ "GO:0003205" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "systema cardiovasculare", - "xrefs" : [ "Wikipedia:Circulatory_system" ] + "pred" : "hasExactSynonym", + "val" : "chamber of heart" + }, { + "pred" : "hasExactSynonym", + "val" : "heart chamber" } ], "xrefs" : [ { - "val" : "AAO:0000959" - }, { - "val" : "CALOHA:TS-2103" - }, { - "val" : "VHOG:0001248" + "val" : "FMA:7095" }, { - "val" : "Wikipedia:Circulatory_system" + "val" : "SCTID:276456008" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6073" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001015", - "lbl" : "musculature", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004176", + "lbl" : "external genitalia", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A subdivision of the muscular system corresponding to a subdisivision of an organism.", - "xrefs" : [ "Wikipedia:Muscular_system", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "The external genitalia are the outer sex organs, such as the penis or vulva in mammals.", + "xrefs" : [ "GO:0035261" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "muscle group" - }, { - "pred" : "hasExactSynonym", - "val" : "muscles set" - }, { - "pred" : "hasExactSynonym", - "val" : "musculature" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "musculi", - "xrefs" : [ "FMA:32558", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of muscles", - "xrefs" : [ "FMA:32558" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of skeletal muscles", - "xrefs" : [ "MA:0000165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle system" + "val" : "external genitalia" }, { "pred" : "hasRelatedSynonym", - "val" : "muscles" + "val" : "external reproductive organ" }, { "pred" : "hasRelatedSynonym", - "val" : "musculature system" + "val" : "external sex organ" } ], "xrefs" : [ { - "val" : "BTO:0000887" - }, { - "val" : "EFO:0001949" - }, { - "val" : "EMAPA:35577" - }, { - "val" : "FMA:32558" - }, { - "val" : "MA:0000165" - }, { - "val" : "NCIT:C13056" - }, { - "val" : "TAO:0000548" - }, { - "val" : "UMLS:C0026845" - }, { - "val" : "VSAO:0005038" - }, { - "val" : "WBbt:0005737" - }, { - "val" : "Wikipedia:Muscular_system" + "val" : "FMA:45643" }, { - "val" : "ZFA:0000548" + "val" : "SCTID:362207005" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "lbl" : "nervous system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004188", + "lbl" : "glomerular epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", - "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] + "val" : "The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.", + "xrefs" : [ "GO:0072010" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neurological system", - "xrefs" : [ "GO:0050877" ] + "val" : "epithelium of glomerulus" }, { - "pred" : "hasNarrowSynonym", - "val" : "nerve net", - "xrefs" : [ "Wikipedia:Nerve_net" ] + "pred" : "hasExactSynonym", + "val" : "epithelium of kidney glomerulus" + }, { + "pred" : "hasExactSynonym", + "val" : "epithelium of renal glomerulus" + }, { + "pred" : "hasExactSynonym", + "val" : "kidney glomerular epithelium", + "xrefs" : [ "MA:0002847" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "systema nervosum", - "xrefs" : [ "Wikipedia:Nervous_system" ] + "val" : "glomerular epithelial cell", + "xrefs" : [ "BTO:0001515" ] } ], "xrefs" : [ { - "val" : "AAO:0000324" - }, { - "val" : "BILA:0000079" - }, { - "val" : "BIRNLEX:844" - }, { - "val" : "BTO:0001484" - }, { - "val" : "CALOHA:TS-1313" - }, { - "val" : "EFO:0000802" - }, { - "val" : "EHDAA2:0001246" - }, { - "val" : "EHDAA:826" - }, { - "val" : "EMAPA:16469" - }, { - "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" - }, { - "val" : "FMA:7157" - }, { - "val" : "GAID:466" - }, { - "val" : "MA:0000016" - }, { - "val" : "MAT:0000026" - }, { - "val" : "MESH:D009420" - }, { - "val" : "MIAA:0000026" - }, { - "val" : "NCIT:C12755" - }, { - "val" : "SCTID:278196006" - }, { - "val" : "TAO:0000396" - }, { - "val" : "UMLS:C0027763" - }, { - "val" : "VHOG:0000402" - }, { - "val" : "WBbt:0005735" - }, { - "val" : "Wikipedia:Nervous_system" - }, { - "val" : "XAO:0000177" + "val" : "BTO:0001515" }, { - "val" : "ZFA:0000396" + "val" : "EMAPA:35458" }, { - "val" : "neuronames:3236" + "val" : "MA:0002847" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check - GO says outer, BTO says inner. Make this a superclass" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "lbl" : "central nervous system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004190", + "lbl" : "renal glomerulus vasculature", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.", - "xrefs" : [ "GO:0021551", "http://www.frontiersinzoology.com/content/7/1/29", "https://sourceforge.net/p/geneontology/ontology-requests/11422/" ] + "val" : "The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.", + "xrefs" : [ "GO:0072012" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasExactSynonym", - "val" : "CNS" + "val" : "glomerulus vasculature", + "xrefs" : [ "OBOL:automatic" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "systema nervosum centrale", - "xrefs" : [ "FMA:55675", "FMA:TA" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "cerebrospinal axis", - "xrefs" : [ "FMA:55675" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neuraxis", - "xrefs" : [ "FMA:55675" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000090" - }, { - "val" : "BAMS:CNS" - }, { - "val" : "BILA:0000080" - }, { - "val" : "BIRNLEX:1099" - }, { - "val" : "BTO:0000227" - }, { - "val" : "CALOHA:TS-0150" - }, { - "val" : "EFO:0000908" - }, { - "val" : "EHDAA2:0000225" - }, { - "val" : "EHDAA:828" - }, { - "val" : "EMAPA:16470" - }, { - "val" : "EMAPA:16754" - }, { - "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" - }, { - "val" : "FMA:55675" - }, { - "val" : "GAID:570" - }, { - "val" : "MA:0000167" - }, { - "val" : "MAT:0000457" - }, { - "val" : "MESH:D002490" - }, { - "val" : "NCIT:C12438" - }, { - "val" : "SCTID:278199004" - }, { - "val" : "TAO:0000012" - }, { - "val" : "UMLS:C0927232" - }, { - "val" : "VHOG:0000293" - }, { - "val" : "Wikipedia:Central_nervous_system" + "val" : "renal glomerulus vascular network", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "XAO:0000215" + "pred" : "hasExactSynonym", + "val" : "renal glomerulus vasculature", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "ZFA:0000012" + "pred" : "hasExactSynonym", + "val" : "vascular network of renal glomerulus", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "neuronames:854" + "pred" : "hasExactSynonym", + "val" : "vasculature of renal glomerulus", + "xrefs" : [ "OBOL:automatic" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -21640,241 +23094,235 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001041", - "lbl" : "foregut", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004198", + "lbl" : "comma-shaped body", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anterior subdivision of a digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron.", + "xrefs" : [ "GO:0072049" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "praeenteron", - "xrefs" : [ "Wikipedia:Foregut" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "proenteron", - "xrefs" : [ "Wikipedia:Foregut" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasExactSynonym", + "val" : "CSB" } ], "xrefs" : [ { - "val" : "AAO:0011042" - }, { - "val" : "BILA:0000085" - }, { - "val" : "BTO:0000507" - }, { - "val" : "EHDAA2:0000557" - }, { - "val" : "EHDAA:520" - }, { - "val" : "EMAPA:16548" - }, { - "val" : "FBbt:00005379" - }, { - "val" : "FMA:45616" - }, { - "val" : "MA:0001526" - }, { - "val" : "NCIT:C34180" - }, { - "val" : "SCTID:361409009" - }, { - "val" : "TGMA:0001014" - }, { - "val" : "UMLS:C0231051" - }, { - "val" : "VHOG:0000285" - }, { - "val" : "Wikipedia:Foregut" + "val" : "EMAPA:27681" }, { - "val" : "XAO:0000232" + "val" : "ZFA:0005588" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001045", - "lbl" : "midgut", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004199", + "lbl" : "S-shaped body", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].", - "xrefs" : [ "GO:0007494", "Wikipedia:Midgut" ] + "val" : "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.", + "xrefs" : [ "GO:0072050" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesenteron", - "xrefs" : [ "Wikipedia:Midgut" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasExactSynonym", + "val" : "SSB" + }, { + "pred" : "hasExactSynonym", + "val" : "stage II nephron", + "xrefs" : [ "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] } ], "xrefs" : [ { - "val" : "BILA:0000086" - }, { - "val" : "BTO:0000863" - }, { - "val" : "EFO:0001950" - }, { - "val" : "EHDAA2:0001185" - }, { - "val" : "EHDAA:983" - }, { - "val" : "EMAPA:16255" - }, { - "val" : "FBbt:00005383" - }, { - "val" : "FMA:45617" - }, { - "val" : "MA:0001564" - }, { - "val" : "NCIT:C34210" - }, { - "val" : "SCTID:361410004" - }, { - "val" : "TGMA:0001036" - }, { - "val" : "UMLS:C0231052" - }, { - "val" : "VHOG:0000290" - }, { - "val" : "Wikipedia:Midgut" + "val" : "EMAPA:27756" }, { - "val" : "XAO:0000103" + "val" : "ZFA:0005589" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" + "val" : "TODO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001046", - "lbl" : "hindgut", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004200", + "lbl" : "kidney pyramid", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The caudalmost subdivision of a digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.", + "xrefs" : [ "GO:0072056", "http://anatomy.uams.edu/anatomyhtml/kidney.html" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "pyramid", + "xrefs" : [ "GO:0072056" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Malpighian pyramid", + "xrefs" : [ "Wikipedia:Renal_pyramids" ] + }, { + "pred" : "hasExactSynonym", + "val" : "renal pyramid", + "xrefs" : [ "Wikipedia:Renal_pyramids" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", + "pred" : "hasRelatedSynonym", + "val" : "Malphigian pyramid", + "xrefs" : [ "BTO:0003926" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Malpighian pyramid" + }, { + "pred" : "hasRelatedSynonym", + "val" : "medullary pyramid" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", + "pred" : "hasRelatedSynonym", + "val" : "pyramid of Malphigi", + "xrefs" : [ "ncithesaurus:Pyramid_of_Malpighi" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "pyramid of Malpighi", + "xrefs" : [ "UBERON:cjm" ] + }, { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "metenteron", - "xrefs" : [ "Wikipedia:Hindgut" ] + "val" : "pyramides renales", + "xrefs" : [ "Wikipedia:Renal_pyramids" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "pyramis renalis", + "xrefs" : [ "BTO:0003926" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "renal medullary region", + "xrefs" : [ "FMA:258870" ] } ], "xrefs" : [ { - "val" : "AAO:0011052" - }, { - "val" : "BILA:0000087" + "val" : "BTO:0003926" }, { - "val" : "BTO:0000510" + "val" : "FMA:258870" }, { - "val" : "EHDAA2:0000779" + "val" : "MA:0001654" }, { - "val" : "EHDAA:975" + "val" : "NCIT:C12886" }, { - "val" : "EMAPA:16715" + "val" : "NCIT:C33436" }, { - "val" : "FBbt:00005384" + "val" : "SCTID:361328001" }, { - "val" : "FMA:45618" + "val" : "UMLS:C0227629" }, { - "val" : "MA:0001527" + "val" : "UMLS:C1514613" }, { - "val" : "NCIT:C34188" + "val" : "Wikipedia:Renal_pyramids" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "SCTID:362856002" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0002449" }, { - "val" : "TGMA:0001020" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0005098" }, { - "val" : "UMLS:C0231053" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "val" : "VHOG:0000459" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" }, { - "val" : "Wikipedia:Hindgut" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" }, { - "val" : "XAO:0000104" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" + "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001048", - "lbl" : "primordium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004202", + "lbl" : "kidney outer medulla outer stripe", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. 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It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesenchyme of nephron", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "XAO:0003043" + "pred" : "hasExactSynonym", + "val" : "nephron mesenchyme", + "xrefs" : [ "OBOL:automatic" ] } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -21882,204 +23330,169 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001049", - "lbl" : "neural tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004209", + "lbl" : "renal vesicle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].", - "xrefs" : [ "Wikipedia:Neural_tube" ] + "val" : "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.", + "xrefs" : [ "GO:0072077" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural primordium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tubus neuralis", - "xrefs" : [ "Wikipedia:Neural_tube" ] + "pred" : "hasExactSynonym", + "val" : "stage I nephron", + "xrefs" : [ "ZFA:0005586", "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] } ], - "xrefs" : [ { - "val" : "AAO:0010617" - }, { - "val" : "BTO:0001057" - }, { - "val" : "CALOHA:TS-2371" - }, { - "val" : "DHBA:10154" - }, { - "val" : "EHDAA2:0001254" - }, { - "val" : "EHDAA:2869" - }, { - "val" : "EHDAA:908" - }, { - "val" : "EMAPA:16164" - }, { - "val" : "EMAPA:16757" - }, { - "val" : "FMA:293882" - }, { - "val" : "MAT:0000069" - }, { - "val" : "MIAA:0000069" - }, { - "val" : "NCIT:C34226" - }, { - "val" : "SCTID:362852000" - }, { - "val" : "TAO:0001135" - }, { - "val" : "UMLS:C0231024" - }, { - "val" : "VHOG:0000307" - }, { - "val" : "Wikipedia:Neural_tube" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. 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Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001637", - "lbl" : "artery", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005167", + "lbl" : "papillary duct", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].", - "xrefs" : [ "AEO:JB" ] + "val" : "The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx.", + "xrefs" : [ "http://encyclopedia.thefreedictionary.com/" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "arterial subtree" + "val" : "papillary duct" }, { "pred" : "hasExactSynonym", - "val" : "arterial tree organ part" + "val" : "papillary duct of kidney" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "arteries", - "xrefs" : [ "TAO:0000005" ] + "val" : "renal papillary duct" }, { "pred" : "hasRelatedSynonym", - "val" : "arterial system" + "val" : "Bellini's duct", + "xrefs" : [ "MP:0011331" ] }, { "pred" : "hasRelatedSynonym", - "val" : "arterial vessel" + "val" : "duct of Bellini" } ], "xrefs" : [ { - "val" : "AAO:0010211" - }, { - "val" : "AEO:0000208" - }, { - "val" : "BTO:0000573" - }, { - "val" : "CALOHA:TS-0054" - }, { - "val" : "EFO:0000814" - }, { - "val" : "EHDAA2:0003253" - }, { - "val" : "EMAPA:35147" - }, { - "val" : "EV:0100026" - }, { - "val" : "FMA:50720" - }, { - "val" : "GAID:468" - }, { - "val" : "MA:0000064" - }, { - "val" : "MAT:0000034" - }, { - "val" : "MESH:D001158" - }, { - "val" : "MIAA:0000034" - }, { - "val" : "NCIT:C12372" - }, { - "val" : "SCTID:362877004" - }, { - "val" : "TAO:0000005" - }, { - "val" : "UMLS:C0003842" - }, { - "val" : "VHOG:0001251" + "val" : "BTO:0004540" }, { - "val" : "Wikipedia:Artery" + "val" : "EMAPA:35655" }, { - "val" : "XAO:0000114" + "val" : "MA:0001646" }, { - "val" : "ZFA:0000005" + "val" : "SCTID:110623009" }, { - "val" : "galen:Artery" + "val" : "Wikipedia:Duct_of_Bellini" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001638", - "lbl" : "vein", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005169", + "lbl" : "interstitial tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the tubular branching vessels that carry blood from the capillaries toward the heart.", - "xrefs" : [ "Wikipedia:Vein" ] + "val" : "Connective tissue between the cellular elements of a structure.", + "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/tissue" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "venous subtree" - }, { - "pred" : "hasBroadSynonym", - "val" : "venous vessel" - }, { "pred" : "hasExactSynonym", - "val" : "venous tree organ part" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vascular element", - "xrefs" : [ "EMAPA:th" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "vena", - "xrefs" : [ "Wikipedia:Vein" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "venae", - "xrefs" : [ "VHOG:0001743" ] + "val" : "interstitium" } ], "xrefs" : [ { - "val" : "AAO:0010212" - }, { - "val" : "AEO:0000209" - }, { - "val" : "BTO:0000234" - }, { - "val" : "CALOHA:TS-1108" - }, { - "val" : "EFO:0000816" - }, { - "val" : "EHDAA2:0003254" - }, { - "val" : "EMAPA:35906" - }, { - "val" : "EV:0100031" - }, { - "val" : "FMA:50723" - }, { - "val" : "GAID:492" - }, { - "val" : "MA:0000067" - }, { - "val" : "MAT:0000037" - }, { - "val" : "MESH:D014680" - }, { - "val" : "MIAA:0000037" - }, { - "val" : "NCIT:C12814" - }, { - "val" : "SCTID:181367001" - }, { - "val" : "TAO:0000082" - }, { - "val" : "UMLS:C0042449" - }, { - "val" : "VHOG:0001743" - }, { - "val" : "Wikipedia:Vein" - }, { - "val" : "XAO:0000115" - }, { - "val" : "ZFA:0000082" + "val" : "FMA:86301" }, { - "val" : "galen:Vein" + "val" : "SCTID:85293002" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check with MA - vein vs venous blood vessel" + "val" : "specify differentia from stroma" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001851", - "lbl" : "cortex", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005172", + "lbl" : "abdomen element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Outermost layer of an organ[WP].", - "xrefs" : [ "Wikipedia:Cortex_(anatomy)" ] + "val" : "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "cortex", - "xrefs" : [ "FMA:61109" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cortex of organ" + "val" : "abdomen organ", + "xrefs" : [ "MA:0000522" ] } ], "xrefs" : [ { - "val" : "EFO:0000383" - }, { - "val" : "EHDAA:9344" - }, { - "val" : "FMA:61109" - }, { - "val" : "Wikipedia:Cortex_(anatomy)" + "val" : "MA:0000522" }, { - "val" : "galen:Cortex" + "val" : "SCTID:272631008" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -23807,56 +25011,24 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "lbl" : "blood plasma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005173", + "lbl" : "abdominal segment element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The liquid component of blood, in which erythrocytes are suspended.", + "val" : "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "plasma", - "xrefs" : [ "MA:0002501" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "portion of plasma", - "xrefs" : [ "FMA:62970" ] - }, { "pred" : "hasExactSynonym", - "val" : "blood plasm" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of blood plasma" + "val" : "abdominal segment organ", + "xrefs" : [ "MA:0000529" ] } ], "xrefs" : [ { - "val" : "BTO:0000131" - }, { - "val" : "CALOHA:TS-0800" - }, { - "val" : "EFO:0001905" - }, { - "val" : "EMAPA:35690" - }, { - "val" : "FMA:62970" - }, { - "val" : "GAID:1178" - }, { - "val" : "MA:0002501" - }, { - "val" : "MAT:0000052" - }, { - "val" : "MESH:D010949" - }, { - "val" : "MIAA:0000052" - }, { - "val" : "NCIT:C13356" - }, { - "val" : "UMLS:C0032105" + "val" : "EMAPA:37062" }, { - "val" : "Wikipedia:Blood_plasma" + "val" : "MA:0000529" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -23864,411 +25036,340 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001979", - "lbl" : "venule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", + "lbl" : "trunk region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins.", - "xrefs" : [ "MESH:A07.231.432.952", "MP:0004125" ] + "val" : "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "venula", - "xrefs" : [ "Wikipedia:Venule" ] + "pred" : "hasExactSynonym", + "val" : "trunk organ", + "xrefs" : [ "MA:0000516" ] } ], "xrefs" : [ { - "val" : "BTO:0002626" - }, { - "val" : "EMAPA:35917" - }, { - "val" : "FMA:63130" - }, { - "val" : "MA:0000071" - }, { - "val" : "MESH:D014699" - }, { - "val" : "NCIT:C12818" - }, { - "val" : "SCTID:341687009" - }, { - "val" : "TAO:0005315" - }, { - "val" : "UMLS:C0042520" - }, { - "val" : "VHOG:0001765" - }, { - "val" : "Wikipedia:Venule" + "val" : "EMAPA:37270" }, { - "val" : "ZFA:0005315" + "val" : "MA:0000516" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001980", - "lbl" : "arteriole", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005178", + "lbl" : "thoracic cavity element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The smallest division of the artery located between the muscular arteries and the capillaries[GO].", - "xrefs" : [ "GO:0014830" ] + "val" : "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "arteriola", - "xrefs" : [ "Wikipedia:Arteriole" ] + "pred" : "hasExactSynonym", + "val" : "thoracic cavity organ", + "xrefs" : [ "MA:0000557" ] } ], "xrefs" : [ { - "val" : "AAO:0010253" - }, { - "val" : "BTO:0001997" - }, { - "val" : "EMAPA:35146" - }, { - "val" : "FMA:63182" - }, { - "val" : "MA:0000063" - }, { - "val" : "MESH:D001160" - }, { - "val" : "NCIT:C12672" - }, { - "val" : "SCTID:337724002" - }, { - "val" : "TAO:0002138" - }, { - "val" : "UMLS:C0003847" - }, { - "val" : "VHOG:0001763" - }, { - "val" : "Wikipedia:Arteriole" + "val" : "EMAPA:37273" }, { - "val" : "ZFA:0005255" + "val" : "MA:0000557" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "lbl" : "blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005179", + "lbl" : "pelvic region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A vessel through which blood circulates in the body.", - "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + "val" : "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "vascular element", - "xrefs" : [ "EMAPA:35993" ] + "pred" : "hasExactSynonym", + "val" : "pelvic element" }, { "pred" : "hasExactSynonym", - "val" : "region of vascular tree organ", - "xrefs" : [ "FMA:50722" ] + "val" : "pelvis organ", + "xrefs" : [ "MA:0000543" ] }, { "pred" : "hasExactSynonym", - "val" : "vascular tree organ region", - "xrefs" : [ "FMA:50722" ] + "val" : "pelvis region organ" + } ], + "xrefs" : [ { + "val" : "EMAPA:37275" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "val" : "MA:0000543" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", + "lbl" : "thoracic segment organ", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "vas sanguineum", - "xrefs" : [ "Wikipedia:Blood_vessel" ] + "val" : "upper body organ", + "xrefs" : [ "MA:0000563" ] } ], "xrefs" : [ { - "val" : "AAO:0011004" - }, { - "val" : "AEO:0000207" - }, { - "val" : "BTO:0001102" - }, { - "val" : "CALOHA:TS-0080" - }, { - "val" : "EFO:0000817" - }, { - "val" : "EHDAA2:0003252" - }, { - "val" : "EHDAA:240" - }, { - "val" : "EMAPA:32743" - }, { - "val" : "EMAPA:35993" - }, { - "val" : "FMA:50722" - }, { - "val" : "FMA:63183" - }, { - "val" : "GAID:169" - }, { - "val" : "MA:0000060" - }, { - "val" : "MAT:0000393" - }, { - "val" : "MESH:D001808" - }, { - "val" : "NCIT:C12679" - }, { - "val" : "NLXANAT:090901" - }, { - "val" : "SCTID:361097006" - }, { - "val" : "TAO:0002137" - }, { - "val" : "UMLS:C0005847" - }, { - "val" : "VHOG:0001250" - }, { - "val" : "Wikipedia:Blood_vessel" - }, { - "val" : "XAO:0001011" + "val" : "EMAPA:37271" }, { - "val" : "ZFA:0005314" + "val" : "MA:0000563" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001982", - "lbl" : "capillary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005185", + "lbl" : "renal medulla collecting duct", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the smallest blood vessels connecting arterioles with venules.", - "xrefs" : [ "ISBN:0073040584", "Wikipedia:Capillary", "https://github.com/obophenotype/uberon/issues/137" ] + "val" : "The portion of the collecting duct that resides in the renal medulla.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood capillary" + "val" : "kidney medulla collecting duct", + "xrefs" : [ "MA:0002935" ] }, { "pred" : "hasExactSynonym", - "val" : "capillary vessel" + "val" : "medullary collecting duct", + "xrefs" : [ "EMAPA:28061" ] } ], "xrefs" : [ { - "val" : "AAO:0010252" - }, { - "val" : "BTO:0002045" - }, { - "val" : "CALOHA:TS-2006" - }, { - "val" : "EFO:0001906" - }, { - "val" : "EMAPA:35198" + "val" : "BTO:0004536" }, { - "val" : "EV:0100035" + "val" : "EMAPA:28061" }, { - "val" : "FMA:63194" + "val" : "EMAPA:35459" }, { - "val" : "MA:0000065" + "val" : "MA:0002935" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005215", + "lbl" : "kidney interstitium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.", + "xrefs" : [ "DOI:10.1038/ki.1991.49", "PMID:18575881", "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "interstitial tissue of kidney" }, { - 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Examples: heart, lung, esophagus, kidney, ovary, spleen.", - "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] + "val" : "Portion of tissue that gives rise to the immature gonad.", + "xrefs" : [ "ZFA:0001262" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "visceral organ", - "xrefs" : [ "RETIRED_EHDAA2:0002201" ] + "val" : "future gonad", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "visceral organ system", - "xrefs" : [ "MA:0000019" ] + "val" : "gonadal primordium", + "xrefs" : [ "ZFA:0001262" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic tissue", - "xrefs" : [ "BTO:0001491" ] + "pred" : "hasExactSynonym", + "val" : "primitive gonad", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "viscera" + "pred" : "hasExactSynonym", + "val" : "undifferentiated gonad", + "xrefs" : [ "ZFA:0001262" ] }, { "pred" : "hasRelatedSynonym", - "val" : "visceral tissue", - "xrefs" : [ "BTO:0001491" ] + "val" : "immature gonad", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { - "val" : "AAO:0010386" - }, { - "val" : "BTO:0001491" - }, { - "val" : "EHDAA:512" - }, { - "val" : "EMAPA:16245" - }, { - "val" : "FMA:7085" - }, { - "val" : "MA:0000019" - }, { - "val" : "MESH:D014781" + "val" : "EFO:0003651" }, { - "val" : "NCIT:C28287" + "val" : "EHDAA:5927" }, { - "val" : "RETIRED_EHDAA2:0002201" + "val" : "EMAPA:17204" }, { - "val" : "SCTID:118760003" + "val" : "RETIRED_EHDAA2:0002148" }, { - "val" : "UMLS:C0042779" + "val" : "TAO:0001262" }, { - "val" : "Wikipedia:Viscus" + "val" : "WBbt:0008366" }, { - "val" : "XAO:0003034" + "val" : "ZFA:0001262" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24338,350 +25428,301 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002078", - "lbl" : "right cardiac atrium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005721", + "lbl" : "pronephric mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.", - "xrefs" : [ "Wikipedia:Right_atrium", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A mesoderm that has the potential to develop into a pronephros.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "comments" : [ "the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 \"Developmental Biology\", PMID:10720431 \"Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm\"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cardiac right atrium" - }, { - "pred" : "hasExactSynonym", - "val" : "heart right atrium", - "xrefs" : [ "MA:0000075" ] - }, { - "pred" : "hasExactSynonym", - "val" : "right atrium", - "xrefs" : [ "VHOG:0000328" ] + "pred" : "hasRelatedSynonym", + "val" : "pronephric anlage", + "xrefs" : [ "XAO:0000264" ] }, { - "pred" : "hasExactSynonym", - "val" : "right atrium of heart" + "pred" : "hasRelatedSynonym", + "val" : "pronephric bulge", + "xrefs" : [ "XAO:0000264" ] }, { - "pred" : "hasExactSynonym", - "val" : "right cardiac atrium" + "pred" : "hasRelatedSynonym", + "val" : "pronephric mesenchyme", + "xrefs" : [ "XAO:0000264" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "atrium dextrum", - "xrefs" : [ "Wikipedia:Right_atrium" ] + "val" : "pronephric primordium", + "xrefs" : [ "XAO:0000264" ] } ], "xrefs" : [ { - "val" : "AAO:0010248" - }, { - "val" : "BTO:0001703" - }, { - "val" : "EHDAA2:0000290" - }, { - "val" : "EMAPA:17321" - }, { - "val" : "FMA:7096" - }, { - "val" : "MA:0000075" - }, { - "val" : "NCIT:C12868" - }, { - "val" : "SCTID:244383003" + "val" : "AAO:0011090" }, { - "val" : "UMLS:C0225844" + "val" : "EFO:0003479" }, { - "val" : "VHOG:0000328" + "val" : "TAO:0000067" }, { - "val" : "Wikipedia:Right_atrium" + "val" : "VHOG:0001239" }, { - "val" : "XAO:0003192" + "val" : "XAO:0000264" }, { - "val" : "galen:RightAtrium" + "val" : "ZFA:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005749", + "lbl" : "glomerular tuft", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The capillary loops of the kidney that normally function as a filtration unit[MP].", + "xrefs" : [ "MP:0005325", "Wikipedia:Glomerulus", "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "glomerular capillary tuft" }, { - 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"val" : "Cardiac chamber in which blood enters the heart.", - "xrefs" : [ "Wikipedia:Heart_atrium", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.", + "xrefs" : [ "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "atria" - }, { - "pred" : "hasExactSynonym", - "val" : "atrium", - "xrefs" : [ "ZFA:0000471" ] + "val" : "caudal portion of nephrogenic cord", + "xrefs" : [ "OBOL:automatic" ] }, { "pred" : "hasExactSynonym", - "val" : "atrium of heart" + "val" : "caudal region of nephrogenic cord", + "xrefs" : [ "OBOL:automatic" ] }, { - 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"val" : "galen:Atrium" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", - "lbl" : "postcranial axial skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "lbl" : "basement membrane of epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", - "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] + "val" : "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.", + "xrefs" : [ "Wikipedia:Basement_membrane", "http://orcid.org/0000-0002-6601-2165" ] }, - 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This is being resolved (see tracker items above). Status: MA - fixed." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "axial skeleton", - "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] + "pred" : "hasExactSynonym", + "val" : "basement membrane of connective tissue", + "xrefs" : [ "FMA:63872" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "post-cranial axial skeleton" + "val" : "membrana basalis", + "xrefs" : [ "Wikipedia:Basement_membrane" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "basement membrane", + "xrefs" : [ "FMA:63872" ] } ], "xrefs" : [ { - "val" : "AAO:0000034" - }, { - "val" : "EFO:0000942" - }, { - "val" : "EHDAA2:0000161" - }, { - "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:37721" - }, { - "val" : "FMA:71221" - }, { - "val" : "MA:0002986" - }, { - "val" : "MAT:0000148" + "val" : "AAO:0010596" }, { - "val" : "MIAA:0000148" + "val" : "FMA:63872" }, { - "val" : "TAO:0000317" + "val" : "GAID:915" }, { - "val" : "VHOG:0000317" + "val" : "NCIT:C13191" }, { - "val" : "VSAO:0000093" + "val" : "SCTID:68989006" }, { - "val" : "XAO:0003073" + "val" : "UMLS:C0004799" }, { - "val" : "ZFA:0000317" + "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002091", - "lbl" : "appendicular skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005777", + "lbl" : "glomerular basement membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].", - "xrefs" : [ "UBERONREF:0000003", "Wikipedia:Appendicular_skeleton", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter.", + "xrefs" : [ "MGI:anna", "MP:0011348" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "appendicular skeleton" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasBroadSynonym", + "val" : "GBM" }, { "pred" : "hasExactSynonym", - "val" : "entire appendicular skeleton", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/59" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasNarrowSynonym", - "val" : "paired fin skeleton" + "val" : "glomerular capillary basement membrane", + "xrefs" : [ "MA:0001659" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "skeleton appendiculare", - "xrefs" : [ "Wikipedia:Appendicular_skeleton" ] + "pred" : "hasExactSynonym", + "val" : "glomerular filtration membrane", + "xrefs" : [ "ZFA:0005285" ] } ], "xrefs" : [ { - "val" : "AAO:0000747" - }, { - "val" : "EFO:0000951" - }, { - "val" : "EMAPA:32729" - }, { - "val" : "FMA:71222" + "val" : "EMAPA:28251" }, { - "val" : "MA:0000290" + "val" : "EMAPA:30965" }, { - "val" : "MAT:0000278" + "val" : "FMA:74274" }, { - "val" : "MIAA:0000278" + "val" : "MA:0001659" }, { - "val" : "NCIT:C49477" + "val" : "NCIT:C32683" }, { - "val" : "SCTID:322050006" + "val" : "SCTID:243897006" }, { - "val" : "UMLS:C0222646" + "val" : "TAO:0005285" }, { - "val" : "VSAO:0000076" + "val" : "UMLS:C0599297" }, { - "val" : "Wikipedia:Appendicular_skeleton" + "val" : "Wikipedia:Glomerular_basement_membrane" }, { - "val" : "XAO:0003166" + "val" : "ZFA:0005285" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", - "lbl" : "trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005792", + "lbl" : "nephric ridge", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.", - "xrefs" : [ "TAO:0001115", "UBERONREF:0000006", "Wikipedia:Torso" ] + "val" : "Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.", + "xrefs" : [ "http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter27/custom2/deluxe-content.html" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracolumbar region" - }, { - "pred" : "hasExactSynonym", - "val" : "torso" - }, { - "pred" : "hasExactSynonym", - "val" : "trunk region", - "xrefs" : [ "XAO:0000054" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "Rumpf", - "xrefs" : [ "BTO:0001493" ] + "val" : "nephric cord", + "xrefs" : [ "VHOG:0001240" ] } ], "xrefs" : [ { - "val" : "AAO:0010339" - }, { - "val" : "BILA:0000116" - }, { - "val" : "BTO:0001493" - }, { - "val" : "CALOHA:TS-1071" - }, { - "val" : "EFO:0000966" - }, { - "val" : "EMAPA:31857" - }, { - "val" : "FMA:7181" - }, { - "val" : "MA:0000004" - }, { - "val" : "MAT:0000296" - }, { - "val" : "MIAA:0000296" - }, { - "val" : "NCIT:C33816" - }, { - "val" : "SCTID:262225004" - }, { - "val" : "TAO:0001115" + "val" : "EHDAA2:0001242" }, { - "val" : "UMLS:C0460005" + "val" : "EHDAA:1015" }, { - "val" : "Wikipedia:Torso" + "val" : "EMAPA:16368" }, { - "val" : "XAO:0000054" + "val" : "VHOG:0001240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ridge vs cord vs nephrogenic cord vs blastema" }, { - "val" : "XAO:0003025" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005856", + "lbl" : "developing mesenchymal condensation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A delimited region of dense mesenchyme within looser mesenchyme.", + "xrefs" : [ "AEO:0000148" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesenchyme condensation", + "xrefs" : [ "EMAPA:25351" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000148" }, { - "val" : "ZFA:0001115" + "val" : "EHDAA2_RETIRED:0003148" }, { - "val" : "galen:Trunk" + "val" : "EHDAA:8979" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24689,208 +25730,165 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002113", - "lbl" : "kidney", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005944", + "lbl" : "axial skeleton plus cranial skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.", - "xrefs" : [ "PMID:25140012", "PMID:35003210", "Wikipedia:Kidney", "http://anatomy.uams.edu/anatomyhtml/kidney.html", "https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do" ] + "val" : "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].", + "xrefs" : [ "FMA:71221", "VSAO:0000056", "Wikipedia:Axial_skeleton", "https://github.com/obophenotype/uberon/issues/44", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasNarrowSynonym", - "val" : "reniculate kidney", - "xrefs" : [ "Wikipedia:Reniculate_kidney" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "skeleton axiale", + "xrefs" : [ "Wikipedia:Axial_skeleton" ] } ], "xrefs" : [ { - "val" : "AAO:0000250" - }, { - "val" : "BTO:0000671" - }, { - "val" : "CALOHA:TS-0510" + "val" : "AAO:0000963" }, { - "val" : "GAID:423" + "val" : "EMAPA:17214" }, { - "val" : "MAT:0000119" + "val" : "MA:0000308" }, { - "val" : "MESH:D007668" + "val" : "NCIT:C32172" }, { - "val" : "MIAA:0000119" + "val" : "SCTID:361725000" }, { - "val" : "UMLS:C0022646" + "val" : "UMLS:C0222645" }, { - "val" : "Wikipedia:Kidney" + "val" : "VSAO:0000056" }, { - "val" : "XAO:0003267" + "val" : "Wikipedia:Axial_skeleton" }, { - "val" : "galen:Kidney" + "val" : "XAO:0004011" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-7655-4833" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-2804-127X" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002120", - "lbl" : "pronephros", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006217", + "lbl" : "cloacal membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].", - "xrefs" : [ "GO:0048793", "Wikipedia:Pronephros" ] + "val" : "The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.", + "xrefs" : [ "MP:0011837", "MP:anna", "Wikipedia:Cloacal_membrane" ] }, - "comments" : [ "Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "pronephric kidney", - "xrefs" : [ "XAO:0002000" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "archinephron", - "xrefs" : [ "BTO:0001541" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic kidney", - "xrefs" : [ "BTO:0001541" ] + "val" : "embryonic cloacal membrane" }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "pronephron", - "xrefs" : [ "BTO:0001541" ] + "val" : "membrana cloacalis", + "xrefs" : [ "Wikipedia:Cloacal_membrane" ] } ], "xrefs" : [ { - "val" : "AAO:0011089" - }, { - "val" : "BTO:0001541" - }, { - "val" : "EFO:0000927" - }, { - "val" : "EHDAA2:0001570" - }, { - "val" : "EHDAA:1017" - }, { - "val" : "EMAPA:16579" - }, { - "val" : "FMA:72170" - }, { - "val" : "MAT:0000117" + "val" : "EHDAA2:0000257" }, { - "val" : "MIAA:0000117" + "val" : "EHDAA:214" }, { - "val" : "NCIT:C34280" + "val" : "EHDAA:2933" }, { - "val" : "SCTID:308804007" + "val" : "EMAPA:16832" }, { - "val" : "TAO:0000151" + "val" : "FMA:295525" }, { - "val" : "UMLS:C0231048" + "val" : "NCIT:C34128" }, { - "val" : "VHOG:0000037" + "val" : "SCTID:308826008" }, { - "val" : "Wikipedia:Pronephros" + "val" : "UMLS:C0231056" }, { - "val" : "XAO:0002000" + "val" : "VHOG:0001198" }, { - "val" : "ZFA:0000151" + "val" : "Wikipedia:Cloacal_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005794" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "lbl" : "hemolymphoid system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", + "lbl" : "notochordal plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", + "xrefs" : [ "VHOG:0001212" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hematolymphoid system" - }, { - "pred" : "hasExactSynonym", - "val" : "lymphomyeloid complex" - }, { - "pred" : "hasRelatedSynonym", - "val" : "haemolymphoid system" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "xrefs" : [ { - "val" : "CALOHA:TS-2018" + "val" : "EHDAA2:0001278" }, { - "val" : "EHDAA2:0004615" + "val" : "EHDAA:264" }, { - "val" : "EMAPA:18765" + "val" : "EMAPA:16101" }, { - "val" : "FMA:74562" + "val" : "NCIT:C34231" }, { - "val" : "MA:0000013" + "val" : "UMLS:C1518429" + }, { + "val" : "VHOG:0001212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ordering; awaiting confirmation from JB" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002201", - "lbl" : "vasculature of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", + "lbl" : "notochordal process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A vasculature that is part of a trunk [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", + "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "torso vascular network", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "torso vasculature", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "chordamesoderm" }, { - "pred" : "hasExactSynonym", - "val" : "trunk vascular network", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "presumptive notochord" + } ], + "xrefs" : [ { + "val" : "EHDAA2:0001279" }, { - "pred" : "hasExactSynonym", - "val" : "trunk vasculature" + "val" : "EHDAA:224" }, { - "pred" : "hasExactSynonym", - "val" : "vascular network of torso", - "xrefs" : [ "OBOL:automatic" ] + "val" : "EMAPA:16102" }, { - "pred" : "hasExactSynonym", - "val" : "vascular network of trunk", - "xrefs" : [ "OBOL:automatic" ] + "val" : "FMA:293135" }, { - "pred" : "hasExactSynonym", - "val" : "vasculature of torso", - "xrefs" : [ "OBOL:automatic" ] - } ], - "xrefs" : [ { - "val" : "FMA:74712" + "val" : "NCIT:C34232" }, { - "val" : "TAO:0005024" + "val" : "UMLS:C1518430" }, { - "val" : "ZFA:0005024" + "val" : "VHOG:0001213" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24898,49 +25896,37 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002204", - "lbl" : "musculoskeletal system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006314", + "lbl" : "bodily fluid", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that consists of the muscular and skeletal systems.", - "xrefs" : [ "VSAO:0000031", "VSAO:curator", "https://github.com/obophenotype/uberon/issues/77" ] + "val" : "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", + "xrefs" : [ "MESH:A12.207", "Wikipedia:Body_fluid" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "fluid" + }, { "pred" : "hasExactSynonym", - "val" : "musculo-skeletal system" + "val" : "body fluid", + "xrefs" : [ "GAID:266" ] } ], "xrefs" : [ { - "val" : "AAO:0010546" - }, { - "val" : "CALOHA:TS-1311" - }, { - "val" : "EMAPA:32714" - }, { - "val" : "EV:0100139" - }, { - "val" : "FMA:7482" - }, { - "val" : "GAID:98" - }, { - "val" : "MA:0002418" - }, { - "val" : "MESH:D009141" - }, { - "val" : "NCIT:C12754" + "val" : "BIRNLEX:20" }, { - "val" : "SCTID:278858007" + "val" : "EMAPA:37441" }, { - "val" : "UMLS:C0026860" + "val" : "FMA:280556" }, { - "val" : "VHOG:0001275" + "val" : "GAID:266" }, { - "val" : "VSAO:0000031" + "val" : "MESH:D001826" }, { - "val" : "Wikipedia:Musculoskeletal_system" + "val" : "Wikipedia:Body_fluid" }, { - "val" : "XAO:0000168" + "val" : "galen:BodyFluid" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24948,109 +25934,76 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002224", - "lbl" : "thoracic cavity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006534", + "lbl" : "renal convoluted tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.", - "xrefs" : [ "UBERON:cjm", "Wikipedia:Thoracic_cavity" ] + "val" : "Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "cavitas thoracis", - "xrefs" : [ "Wikipedia:Thoracic_cavity" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cavity of chest" - }, { - "pred" : "hasExactSynonym", - "val" : "cavity of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "chest cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "pectoral cavity" - }, { "pred" : "hasExactSynonym", - "val" : "space of thoracic compartment", - "xrefs" : [ "FMA:7565" ] + "val" : "convoluted tubule" }, { "pred" : "hasExactSynonym", - "val" : "thoracic lumen" + "val" : "kidney convoluted tubule", + "xrefs" : [ "MA:0001665" ] } ], "xrefs" : [ { - "val" : "EMAPA:36497" - }, { - "val" : "FMA:7565" - }, { - "val" : "GAID:93" - }, { - "val" : "MA:0000032" + "val" : "EMAPA:35725" }, { - "val" : "MESH:D035423" + "val" : "MA:0001665" }, { - "val" : "NCIT:C12905" + "val" : "NCIT:C49479" }, { - "val" : "SCTID:243949006" + "val" : "SCTID:361333002" }, { - "val" : "UMLS:C0230139" + "val" : "UMLS:C1707510" }, { - "val" : "Wikipedia:Thoracic_cavity" + "val" : "Wikipedia:Convoluted_tubule" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002303", - "lbl" : "juxtaglomerular apparatus", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006542", + "lbl" : "outer medulla outer stripe loop of Henle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP].", - "xrefs" : [ "GO:0072206", "Wikipedia:Juxtaglomerular_apparatus" ] + "val" : "A loop of Henle that is part of a kidney outer medulla outer stripe.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "complexus juxtaglomerularis" + "xrefs" : [ { + "val" : "EMAPA:29665" }, { - "pred" : "hasExactSynonym", - "val" : "juxtaglomerular complex", - "xrefs" : [ "MP:0002829" ] + "val" : "MA:0002630" } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006544", + "lbl" : "kidney vasculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vasculature that is part of a kidney.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "xrefs" : [ { - "val" : "BTO:0005157" - }, { - "val" : "EMAPA:30449" - }, { - "val" : "FMA:83599" - }, { - "val" : "GAID:432" - }, { - "val" : "MA:0002546" - }, { - "val" : "MESH:D007606" - }, { - "val" : "NCIT:C32891" - }, { - "val" : "SCTID:362219002" + "val" : "EMAPA:28457" }, { - "val" : "UMLS:C0022445" + "val" : "TAO:0005305" }, { - "val" : "Wikipedia:Juxtaglomerular_apparatus" + "val" : "ZFA:0005305" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -25061,489 +26014,225 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002319", - "lbl" : "mesangium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006553", + "lbl" : "renal duct", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries.", - "xrefs" : [ "Wikipedia:Mesangium", "https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/13/" ] + "val" : "A tube in the kidney that collect and transport urine.", + "xrefs" : [ "ZFIN:ZDB-PUB-071029-9" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "xrefs" : [ { - "val" : "BTO:0002494" - }, { - "val" : "EMAPA:36561" - }, { - "val" : "FMA:84139" - }, { - "val" : "MA:0002617" - }, { - "val" : "NCIT:C33101" - }, { - "val" : "UMLS:C0017655" + "val" : "TAO:0005289" }, { - "val" : "Wikipedia:Mesangium" + "val" : "ZFA:0005289" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002321", - "lbl" : "extraglomerular mesangium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006555", + "lbl" : "excretory tube", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus.", - "xrefs" : [ "ISBN:0-683-40008-8", "MP:0011340" ] + "val" : "A tube that is part of a excretory system.", + "xrefs" : [ "OBOL:automatic" ] }, - "comments" : [ "EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "EMAPA:28278" - }, { - "val" : "FMA:84141" - }, { - "val" : "MA:0002602" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", - "lbl" : "coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006595", + "lbl" : "presumptive endoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. 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The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. 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Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] + }, + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "AAO:0000098" - }, { - "val" : "BTO:0000421" - }, { - "val" : "CALOHA:TS-2009" - }, { - "val" : "EFO:0000952" - }, { - "val" : "EMAPA:35251" - }, { - "val" : "FMA:9640" - }, { - "val" : "GAID:100" - }, { - "val" : "MA:0000011" - }, { - "val" : "MAT:0000301" - }, { - "val" : "MESH:D003238" - }, { - "val" : "MIAA:0000301" - }, { - "val" : "NCIT:C12374" - }, { - "val" : "SCTID:361919005" - }, { - "val" : "TAO:0001641" + "val" : "BILA:0000010" }, { - "val" : "UMLS:C0009780" + "val" : "CARO:0001002" }, { - "val" : "VSAO:0000017" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "XAO:0001017" + "val" : "FMA:24137" }, { - "val" : "ZFA:0001632" + "val" : "NCIT:C34022" }, { - "val" : "galen:ConnectiveTissue" + "val" : "UMLS:C1515977" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "lbl" : "muscle tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "lbl" : "cardiogenic splanchnic mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", - "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] + "val" : "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].", + "xrefs" : [ "XAO:0000235", "http://www.drugs.com/dict/cardiogenic-mesoderm.html", "https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7" ] }, - "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] - }, { "pred" : "hasExactSynonym", - "val" : "textus muscularis" - } ], - "xrefs" : [ { - "val" : "AAO:0000306" + "val" : "cardiogenic splanchnopleure", + "xrefs" : [ "EHDAA2:0000214" ] }, { - "val" : "AEO:0000122" + "pred" : "hasRelatedSynonym", + "val" : "cardiac mesoderm", + "xrefs" : [ "XAO:0000235" ] }, { - "val" : "CALOHA:TS-0642" + "pred" : "hasRelatedSynonym", + "val" : "cardiogenic mesoderm", + "xrefs" : [ "http://www.drugs.com/dict/cardiogenic-mesoderm.html" ] }, { - "val" : "EHDAA2:0003122" + "pred" : "hasRelatedSynonym", + "val" : "cardiogenic region", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "EMAPA:32715" + "pred" : "hasRelatedSynonym", + "val" : "heart primordia", + "xrefs" : [ "XAO:0000235" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011021" }, { - "val" : "FMA:9641" + "val" : "BILA:0000051" }, { - "val" : "MA:0002437" + "val" : "EFO:0000315" }, { - "val" : "MESH:D009132" + "val" : "EHDAA2:0000214" }, { - "val" : "NCIT:C12435" + "val" : "EHDAA:385" }, { - "val" : "SCTID:91727004" + "val" : "FMA:293143" }, { - "val" : "UMLS:C2328219" + "val" : "SCTID:360387000" }, { - "val" : "Wikipedia:Muscle_tissue" + "val" : "VHOG:0001641" }, { - "val" : "galen:MuscleTissue" + "val" : "XAO:0000235" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider FBbt:00005541 ! cardiogenic mesoderm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "review EHDAA2 placement" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", + "lbl" : "cleaving embryo", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "Organism at the cleavage stage.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "xrefs" : [ { + "val" : "BILA:0000058" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", + "lbl" : "presumptive gut", + "type" : "CLASS", + "meta" : { "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "haematological system" + "val" : "future digestive tract" }, { "pred" : "hasExactSynonym", - "val" : "haemopoietic system" + "val" : "future digestive tube" }, { "pred" : "hasExactSynonym", - "val" : "organa haemopoietica" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Blutbildungssystem", - "xrefs" : [ "BTO:0000570" ] + "val" : "future gut" }, { - "pred" : "hasRelatedSynonym", - "val" : "haematopoietic system" + "pred" : "hasExactSynonym", + "val" : "primitive gut" }, { "pred" : "hasRelatedSynonym", - "val" : "hematological system" + "val" : "embryonic digestive tube" }, { "pred" : "hasRelatedSynonym", - "val" : "hematolymphoid system" + "val" : "primordial digestive tube" }, { "pred" : "hasRelatedSynonym", - "val" : "hemopoietic system" + "val" : "primordial gut" } ], "xrefs" : [ { - "val" : "AAO:0011002" - }, { - "val" : "BTO:0000570" - }, { - "val" : "CALOHA:TS-0449" - }, { - "val" : "EFO:0000798" - }, { - "val" : "EMAPA:35402" - }, { - "val" : "EV:0100045" - }, { - "val" : "FMA:9667" - }, { - "val" : "GAID:1008" - }, { - "val" : "MA:0002434" - }, { - "val" : "MAT:0000022" - }, { - "val" : "MESH:D006413" - }, { - "val" : "MIAA:0000022" - }, { - "val" : "NCIT:C12909" - }, { - "val" : "SCTID:362587009" - }, { - "val" : "TAO:0005023" - }, { - "val" : "UMLS:C0018957" - }, { - "val" : "VHOG:0001624" + "val" : "BILA:0000084" }, { - "val" : "Wikipedia:Haematopoiesis" + "val" : "NCIT:C34268" }, { - "val" : "XAO:0000122" + "val" : "SCTID:360394002" }, { - "val" : "ZFA:0005023" + "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002417", - "lbl" : "abdominal segment of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007100", + "lbl" : "primary circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The abdominal segment of the torso.", - "xrefs" : [ "Wikipedia:Lumbar" ] + "val" : "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].", + "xrefs" : [ "GO:0007507" ] }, + "comments" : [ "Gene notes: Bmp, Nkx, Gata" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "abdomen/pelvis/perineum", - "xrefs" : [ "MA:0000021" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "lower body", - "xrefs" : [ "MA:0000021" ] + "pred" : "hasNarrowSynonym", + "val" : "dorsal tube", + "xrefs" : [ "Wikipedia:Heart" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "lower trunk", - "xrefs" : [ "FMA:259211" ] + "pred" : "hasNarrowSynonym", + "val" : "heart", + "xrefs" : [ "GO:0007507" ] }, { "pred" : "hasRelatedSynonym", - "val" : "lumbar region", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "adult heart", + "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "EMAPA:35104" - }, { - "val" : "FMA:259211" - }, { - "val" : "MA:0000021" - }, { - "val" : "SCTID:362875007" + "val" : "TADS:0000147" }, { - "val" : "Wikipedia:Lumbar" + "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -25865,86 +26496,54 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", - "lbl" : "epiblast (generic)", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007135", + "lbl" : "neural keel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", - "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] + "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.", + "xrefs" : [ "ZFIN:ZDB-PUB-961014-576" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epiblast", - "xrefs" : [ "VHOG:0000243" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocyst" - }, { "pred" : "hasRelatedSynonym", - "val" : "ectoblast", - "xrefs" : [ "MP:0003886" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epiblastus", - "xrefs" : [ "Wikipedia:Epiblast" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "primitive ectoderm", - "xrefs" : [ "VHOG:0000243" ] + "val" : "presumptive central nervous system", + "xrefs" : [ "ZFA:0000131" ] } ], "xrefs" : [ { - "val" : "BTO:0004593" - }, { - "val" : "FMA:296704" - }, { - "val" : "MAT:0000067" - }, { - "val" : "MIAA:0000067" + "val" : "EFO:0003497" }, { - "val" : "VHOG:0000243" + "val" : "TAO:0000131" }, { - "val" : "Wikipedia:Epiblast" + "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007282", + "lbl" : "presumptive segmental plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] + "val" : "A presumptive structure that has the potential to develop into a presomitic mesoderm.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "presumptive segmental plates", + "xrefs" : [ "ZFA:0000053" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" + "val" : "EFO:0003421" }, { - "val" : "NCIT:C34007" + "val" : "TAO:0000053" }, { - "val" : "galen:Cavity" + "val" : "ZFA:0000053" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -25952,104 +26551,65 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007284", + "lbl" : "presumptive neural plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "A presumptive structure that has the potential to develop into a neural plate.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segmental plate" + "val" : "prospective neuroectoderm", + "xrefs" : [ "ZFA:0000063" ] }, { "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] + "val" : "prospective vegetal ectoderm", + "xrefs" : [ "ZFA:0000063" ] } ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" + "val" : "EFO:0003424" }, { - "val" : "XAO:0000057" + "val" : "TAO:0000063" }, { - "val" : "ZFA:0000279" + "val" : "ZFA:0000063" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003060", - "lbl" : "pronephric duct", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007285", + "lbl" : "presumptive paraxial mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].", - "xrefs" : [ "Wikipedia:Pronephric_duct" ] + "val" : "The part of the blastula that has the potential to develop into a paraxial mesoderm.", + "xrefs" : [ "UBERON:cjm", "https://github.com/obophenotype/uberon/issues/1277" ] }, - "comments" : [ "The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "archinephric duct", - "xrefs" : [ "VHOG:0000082" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "ductus pronephricus", - "xrefs" : [ "Wikipedia:Pronephric_duct" ] + "pred" : "hasExactSynonym", + "val" : "future paraxial mesenchyme", + "xrefs" : [ "UBERON:cjm" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "pronephric ducts", - "xrefs" : [ "ZFA:0000150" ] + "pred" : "hasExactSynonym", + "val" : "future paraxial mesoderm" } ], "xrefs" : [ { - "val" : "AAO:0011088" - }, { - "val" : "NCIT:C34279" - }, { - "val" : "SCTID:361406002" - }, { - "val" : "TAO:0000150" - }, { - "val" : "UMLS:C1283945" + "val" : "EFO:0003443" }, { - "val" : "Wikipedia:Pronephric_duct" + "val" : "TAO:0000591" }, { - "val" : "XAO:0000063" + "val" : "XAO:0004134" }, { - "val" : "ZFA:0000150" + "val" : "ZFA:0000591" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26057,60 +26617,26 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007297", + "lbl" : "presumptive pronephric mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. 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From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].", - "xrefs" : [ "Wikipedia:Sclerotome", "XB:curator", "https://github.com/obophenotype/uberon/issues/316" ] + "val" : "Anatomical system that consists of all blood and lymph vessels.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "sclerotomes", - "xrefs" : [ "TAO:0001080" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "sclerotomus", - "xrefs" : [ "Wikipedia:Sclerotome" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "xrefs" : [ { - "val" : "AAO:0010571" - }, { - "val" : "AEO:0000212" - }, { - "val" : "EHDAA2:0003439" - }, { - "val" : "EMAPA:31159" - }, { - "val" : "FMA:295652" - }, { - "val" : "NCIT:C34287" + "val" : "BTO:0001085" }, { - "val" : "TAO:0001080" + "val" : "CALOHA:TS-2053" }, { - "val" : "UMLS:C0183176" + "val" : "EHDAA2:0004520" }, { - "val" : "VHOG:0000680" + "val" : "EMAPA:35905" }, { - "val" : "Wikipedia:Sclerotome" + "val" : "MA:0002718" }, { - "val" : "XAO:0000397" + "val" : "NCIT:C33854" }, { - "val" : "ZFA:0001080" + "val" : "UMLS:C0489903" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with vasculature" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", - "lbl" : "compound organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007823", + "lbl" : "appendage girdle region", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", - "xrefs" : [ "CARO:0000024" ] + "val" : "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).", + "xrefs" : [ "UBERONREF:0000003", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "organ" - } ], - "xrefs" : [ { - "val" : "AAO:0010015" - }, { - "val" : "AEO:0000024" - }, { - "val" : "BILA:0000024" - }, { - "val" : "CARO:0000024" - }, { - "val" : "EHDAA2:0003024" + "pred" : "hasBroadSynonym", + "val" : "girdle" }, { - "val" : "HAO:0000024" + "pred" : "hasBroadSynonym", + "val" : "girdle region" }, { - "val" : "TADS:0000598" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "fin girdle" }, { - "val" : "TAO:0000496" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "fin girdle region" }, { - "val" : "TGMA:0001837" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "limb girdle" }, { - "val" : "VHOG:0001723" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "limb girdle region" + } ], + "xrefs" : [ { + "val" : "EMAPA:37854" }, { - "val" : "XAO:0003041" + "val" : "FMA:24874" }, { - "val" : "ZFA:0000496" + "val" : "VSAO:0000303" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007824" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "lbl" : "mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007832", + "lbl" : "pelvic girdle skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.", - "xrefs" : [ "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up", "https://en.wikipedia.org/wiki/Mesenchyme", "https://github.com/obophenotype/uberon/issues/1641" ] + "val" : "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.", + "xrefs" : [ "VSAO:0000155", "Wikipedia:Pelvis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "mesenchymal tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "mesenchyme tissue" + "val" : "pelvic girdle skeleton", + "xrefs" : [ "VSAO:0000155" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of mesenchymal tissue" + "val" : "skeletal parts of pelvic girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of mesenchyme tissue" + "val" : "skeleton of pelvic girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", "pred" : "hasRelatedSynonym", - "val" : "mesenchyma", - "xrefs" : [ "Wikipedia:Mesenchyme" ] + "val" : "pelvic girdle", + "xrefs" : [ "VSAO:0000155" ] } ], "xrefs" : [ { - "val" : "AAO:0010427" + "val" : "AAO:0000426" }, { - "val" : "AEO:0000145" + "val" : "AAO:0000768" }, { - "val" : "BTO:0001393" + "val" : "EFO:0000947" }, { - "val" : "CALOHA:TS-0620" + "val" : "EHDAA2:0001426" }, { - "val" : "EHDAA2:0003145" + "val" : "EHDAA:7149" }, { - "val" : "EV:0100007" + "val" : "EHDAA:8324" }, { - "val" : "NCIT:C13301" + "val" : "EMAPA:18028" }, { - "val" : "TAO:0000393" + "val" : "FMA:87592" }, { - "val" : "UMLS:C0162415" + "val" : "MAT:0000182" }, { - "val" : "VHOG:0000170" + "val" : "MIAA:0000182" }, { - "val" : "Wikipedia:Mesenchyme" + "val" : "TAO:0000565" }, { - "val" : "XAO:0003046" + "val" : "VHOG:0000305" }, { - "val" : "ZFA:0000393" + "val" : "VSAO:0000155" + }, { + "val" : "Wikipedia:Pelvis" + }, { + "val" : "XAO:0003064" + }, { + "val" : "ZFA:0000565" + }, { + "val" : "galen:PelvicGirdle" + }, { + "val" : "http://people.eku.edu/ritchisong/pectoralgirdles.gif" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" + "val" : "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003133", - "lbl" : "reproductive organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0008987", + "lbl" : "renal parenchyma", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organ involved in reproduction.", - "xrefs" : [ "UBERON:xp" ] + "val" : "The functional tissue of the kidney, consisting of the nephrons.", + "xrefs" : [ "BTO:0003604" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "genital organ" - }, { - "pred" : "hasExactSynonym", - "val" : "reproductive system organ" - }, { - "pred" : "hasExactSynonym", - "val" : "sex organ" + "val" : "parenchyma of kidney", + "xrefs" : [ "FMA:15574" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "genitalia" + "val" : "kidney parenchyma", + "xrefs" : [ "BTO:0003604" ] } ], "xrefs" : [ { - "val" : "EMAPA:37731" - }, { - "val" : "MA:0001752" - }, { - "val" : "MESH:D005835" - }, { - "val" : "NCIT:C25177" - }, { - "val" : "SCTID:128181006" - }, { - "val" : "TGMA:0000591" + "val" : "BTO:0003604" }, { - "val" : "UMLS:C0017420" + "val" : "FMA:15574" }, { - "val" : "WBbt:0008422" + "val" : "SCTID:29704000" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26732,49 +27028,30 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003220", - "lbl" : "metanephric mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009035", + "lbl" : "renal straight tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].", - "xrefs" : [ "GO:0072075", "Wikipedia:Metanephric_blastema" ] + "val" : "Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 \"Developmental Biology\"]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "metanephric blastema", - "xrefs" : [ "Wikipedia:Metanephric_blastema" ] - }, { - "pred" : "hasExactSynonym", - "val" : "metanephric mesoderm", - "xrefs" : [ "Wikipedia:Metanephric_blastema" ] - }, { - "pred" : "hasExactSynonym", - "val" : "metanephrogenic mesenchyme", - "xrefs" : [ "EHDAA:5021" ] + "val" : "kidney straight tubule", + "xrefs" : [ "MA:0002634" ] }, { "pred" : "hasExactSynonym", - "val" : "metanephros associated mesenchyme", - "xrefs" : [ "RETIRED_EHDAA2:0001139" ] + "val" : "straight tubule" } ], "xrefs" : [ { - "val" : "EHDAA2:0004062" - }, { - "val" : "EHDAA:4041" - }, { - "val" : "EHDAA:5021" - }, { - "val" : "EHDAA:5915" - }, { - "val" : "EMAPA:17375" + "val" : "EMAPA:37489" }, { - "val" : "SCTID:361529008" + "val" : "MA:0002634" }, { - "val" : "VHOG:0000540" + "val" : "SCTID:245151008" }, { - "val" : "Wikipedia:Metanephric_blastema" + "val" : "Wikipedia:Tubuli_seminiferi_recti" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26782,55 +27059,107 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003479", - "lbl" : "thoracic cavity vein", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", + "lbl" : "entire embryonic mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A vein that is part of a thoracic cavity [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Sum total of mesenchyme in the embryo.", + "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cavity of chest vein", - "xrefs" : [ "OBOL:automatic" ] + "xrefs" : [ { + "val" : "EHDAA2:0001113" }, { - "pred" : "hasExactSynonym", - "val" : "cavity of thorax vein", - "xrefs" : [ "OBOL:automatic" ] + "val" : "EHDAA:177" }, { - "pred" : "hasExactSynonym", - "val" : "chest cavity vein", - "xrefs" : [ "OBOL:automatic" ] + "val" : "EMAPA:16097" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" }, { - "pred" : "hasExactSynonym", - "val" : "pectoral cavity vein", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003313" }, { - "pred" : "hasExactSynonym", - "val" : "vein of cavity of chest", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009196", + "lbl" : "indifferent external genitalia", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], + "xrefs" : [ { + "val" : "EHDAA2:0004021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009201", + "lbl" : "nephric duct", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A nephric duct is a tube that drains a primitive kidney[GO].", + "xrefs" : [ "GO:0072176" ] + }, + "comments" : [ "pronephric duct or mesonephric duct" ], + "xrefs" : [ { + "val" : "EMAPA:16577" }, { + "val" : "Wikipedia:Wolffian_duct" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", + "lbl" : "subdivision of trunk", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "vein of cavity of thorax", - "xrefs" : [ "OBOL:automatic" ] + "val" : "region of trunk", + "xrefs" : [ "FMA:25054" ] }, { "pred" : "hasExactSynonym", - "val" : "vein of chest cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "trunk subdivision", + "xrefs" : [ "FMA:25054" ] + } ], + "xrefs" : [ { + "val" : "FMA:25054" }, { + "val" : "SCTID:22943007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", + "lbl" : "trunk paraxial mesoderm", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "vein of pectoral cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "trunk and cervical paraxial mesenchyme", + "xrefs" : [ "EHDAA2:0002094" ] }, { - "pred" : "hasExactSynonym", - "val" : "vein of thoracic cavity", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "trunk paraxial mesenchyme", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] } ], "xrefs" : [ { - "val" : "EMAPA:37242" - }, { - "val" : "MA:0001903" + "val" : "EHDAA2:0002094" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26838,21 +27167,43 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003497", - "lbl" : "abdomen blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009773", + "lbl" : "renal tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of an abdomen [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.", + "xrefs" : [ "DOI:10.1371/journal.pone.0099864", "GO:0061333", "GOC:dph", "GOC:mtg_kidney_jan10" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood vessel of abdomen", - "xrefs" : [ "OBOL:automatic" ] + "val" : "renal tubule (generic)", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "tubule of excretory system", + "xrefs" : [ "OBOL:automatic", "https://orcid.org/0000-0002-6601-2165" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009856", + "lbl" : "sac", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "pouch" + }, { + "pred" : "hasRelatedSynonym", + "val" : "diverticulum" } ], "xrefs" : [ { - "val" : "MA:0000518" + "val" : "galen:Diverticulum" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26860,20 +27211,22 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003509", - "lbl" : "arterial blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "lbl" : "anterior lateral plate mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "only in MA - supertype of artery, arteriole, aorta." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "ALPM", + "xrefs" : [ "ZFA:0005041" ] + } ], "xrefs" : [ { - "val" : "EMAPA:35144" + "val" : "EFO:0003704" }, { - "val" : "MA:0000061" + "val" : "TAO:0005041" + }, { + "val" : "ZFA:0005041" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26881,246 +27234,269 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003513", - "lbl" : "trunk blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009885", + "lbl" : "interlobar artery", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of a trunk [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "An artery that supplies a renal lobe.", + "xrefs" : [ "Wikipedia:Interlobar_arteries", "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "blood vessel of torso", - "xrefs" : [ "OBOL:automatic" ] + "val" : "arteriae interlobares renis", + "xrefs" : [ "FMA:TA" ] }, { "pred" : "hasExactSynonym", - "val" : "blood vessel of trunk", - "xrefs" : [ "OBOL:automatic" ] + "val" : "interlobar artery of kidney", + "xrefs" : [ "FMA:71637" ] }, { "pred" : "hasExactSynonym", - "val" : "torso blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "kidney interlobar artery" + }, { + "pred" : "hasExactSynonym", + "val" : "renal interlobar artery", + "xrefs" : [ "MP:0011355" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "arteriae interlobares renis", + "xrefs" : [ "Wikipedia:Interlobar_arteries" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "interlobar arteries of kidney", + "xrefs" : [ "FMA:71637" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of interlobar arteries of kidney", + "xrefs" : [ "FMA:71637" ] } ], "xrefs" : [ { - "val" : "EMAPA:37237" + "val" : "EMAPA:37091" }, { - "val" : "MA:0000511" + "val" : "FMA:71637" + }, { + "val" : "SCTID:62802007" + }, { + "val" : "Wikipedia:Interlobar_arteries" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003517", - "lbl" : "kidney blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009912", + "lbl" : "anatomical lobe", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of a kidney [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "A portion of an organ, such as the liver, lung, breast, or brain.", + "xrefs" : [ "ncithesaurus:Lobe" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "blood vessel of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "lobus", + "xrefs" : [ "FMA:45728", "FMA:TA" ] } ], "xrefs" : [ { - "val" : "MA:0001682" + "val" : "FMA:45728" }, { - "val" : "TAO:0005306" + "val" : "NCIT:C13393" }, { - "val" : "ZFA:0005306" + "val" : "UMLS:C0796494" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003519", - "lbl" : "thoracic cavity blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009913", + "lbl" : "renal lobe", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of a thoracic cavity [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP].", + "xrefs" : [ "MP:0011381", "Wikipedia:Renal_lobe" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood vessel of cavity of chest", - "xrefs" : [ "OBOL:automatic" ] + "val" : "kidney lobe", + "xrefs" : [ "MP:0011381" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "blood vessel of cavity of thorax", - "xrefs" : [ "OBOL:automatic" ] + "val" : "lobi renalis", + "xrefs" : [ "Wikipedia:Renal_lobe" ] }, { "pred" : "hasExactSynonym", - "val" : "blood vessel of chest cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "lobus renalis", + "xrefs" : [ "http://www.mondofacto.com/facts/dictionary?lobus+renalis" ] }, { - "pred" : "hasExactSynonym", - "val" : "blood vessel of pectoral cavity", - "xrefs" : [ "OBOL:automatic" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "lobi renales", + "xrefs" : [ "Wikipedia:Renal_lobe" ] + } ], + "xrefs" : [ { + "val" : "FMA:17881" }, { - "pred" : "hasExactSynonym", - "val" : "blood vessel of thoracic cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "NCIT:C32894" }, { - "pred" : "hasExactSynonym", - "val" : "cavity of chest blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "UMLS:C0736382" }, { - "pred" : "hasExactSynonym", - "val" : "cavity of thorax blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Wikipedia:Renal_lobe" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "todo - add has_part relationships." }, { - "pred" : "hasExactSynonym", - "val" : "chest cavity blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "pectoral cavity blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { - "val" : "EMAPA:37240" + "val" : "CARO:0010000" }, { - "val" : "MA:0000554" + "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003527", - "lbl" : "kidney capillary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010199", + "lbl" : "bona-fide anatomical boundary", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A capillary that is part of a kidney [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "An anatomical boundary that corresponds to some physical discontinuity.", + "xrefs" : [ "CARO:0001004" ] + }, + "comments" : [ "One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "CARO:0001004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010227", + "lbl" : "future cardiac atrium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.", + "xrefs" : [ "ZFA:0001718" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood capillary of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary vessel of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "kidney blood capillary", - "xrefs" : [ "OBOL:automatic" ] + "val" : "presumptive atrium heart tube", + "xrefs" : [ "ZFA:0001718" ] }, { "pred" : "hasExactSynonym", - "val" : "kidney capillary vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "primordial atrium", + "xrefs" : [ "FMA:71005" ] }, { "pred" : "hasExactSynonym", - "val" : "renal capillary", - "xrefs" : [ "OBOL:automatic" ] + "val" : "primordial cardiac atrium", + "xrefs" : [ "FMA:71005" ] } ], "xrefs" : [ { - "val" : "EMAPA:31443" + "val" : "FMA:71005" }, { - "val" : "MA:0002586" + "val" : "TAO:0002228" }, { - "val" : "SCTID:275409003" + "val" : "ZFA:0001718" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003644", - "lbl" : "kidney arterial blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "lbl" : "structure with developmental contribution from neural crest", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An arterial blood vessel that is part of a kidney [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "An anatomical structure that has some part that develops from the neural crest.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "kidney arterial system", - "xrefs" : [ "EMAPA:31436" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:31436" - }, { - "val" : "MA:0002578" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003835", - "lbl" : "abdominal segment blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010316", + "lbl" : "germ layer / neural crest", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "abdominal segment of trunk blood vessel", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "blood vessel of abdominal segment of trunk", - "xrefs" : [ "OBOL:automatic" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37057" - }, { - "val" : "MA:0000524" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "lbl" : "future coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010371", + "lbl" : "ecto-epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Epithelium composed of cells that develops from the ectoderm[FMA,modified].", + "xrefs" : [ "FMA:69064" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "future coelomic cavity lumen" - }, { - "pred" : "hasRelatedSynonym", - "val" : "body cavity precursor" + "val" : "ectoderm-derived epithelium" + } ], + "xrefs" : [ { + "val" : "FMA:69064" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27128,61 +27504,46 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", - "lbl" : "intraembryonic coelom", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010377", + "lbl" : "mesenchyme from somatopleure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", - "xrefs" : [ "MGI:anna", "MP:0012187" ] + "val" : "Mesenchyme that develops_from a somatopleure.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "somatic coelom", - "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] - } ], "xrefs" : [ { - "val" : "EHDAA:251" - }, { - "val" : "EMAPA:16088" - }, { - "val" : "NCIT:C34195" - }, { - "val" : "UMLS:C1512940" - }, { - "val" : "VHOG:0000316" - }, { - "val" : "Wikipedia:Intraembryonic_coelom" + "val" : "EHDAA2:0001120" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" + "val" : "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "lbl" : "stroma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010523", + "lbl" : "microcirculatory vessel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.", + "xrefs" : [ "MESH:A07.231.432", "ZFA:0005251", "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "stromal connective tissue" + "val" : "microcirculatory vessels", + "xrefs" : [ "TAO:0005251" ] } ], "xrefs" : [ { - "val" : "FMA:81494" + "val" : "MESH:D055806" }, { - "val" : "NCIT:C67387" + "val" : "TAO:0005251" }, { - "val" : "UMLS:C0927195" + "val" : "ZFA:0005251" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27190,24 +27551,26 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", - "lbl" : "epithelial tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010532", + "lbl" : "primitive nephron", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", - "xrefs" : [ "GO:0060562", "PMID:12526790" ] + "val" : "An epithelial tube that is fated to become a nephron.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial or endothelial tube" - } ], - "xrefs" : [ { - "val" : "AEO:0000114" + "pred" : "hasBroadSynonym", + "val" : "developing nephron" }, { - "val" : "EHDAA2:0003114" + "pred" : "hasBroadSynonym", + "val" : "primitive nephron" }, { - "val" : "FBbt:00007474" + "pred" : "hasExactSynonym", + "val" : "future nephron" + }, { + "pred" : "hasExactSynonym", + "val" : "presumptive nephron" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27215,511 +27578,439 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003918", - "lbl" : "kidney mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010536", + "lbl" : "nephron progenitor", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].", - "xrefs" : [ "GO:0072074" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of kidney" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "check this" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003920", - "lbl" : "venous blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010707", + "lbl" : "appendage girdle complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that carries blood from the capillaries toward the heart.", - "xrefs" : [ "http://www.thefreedictionary.com/venous+blood+vessel" ] + "val" : "An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton", "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Compare to: vein" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segment of venous tree organ", - "xrefs" : [ "FMA:86188" ] + "val" : "appendage complex", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "venous tree organ segment", - "xrefs" : [ "FMA:86188" ] + "val" : "appendage-girdle complex", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "appendage/girdle complex", + "xrefs" : [ "VSAO:0000214" ] + }, { + "pred" : "hasExactSynonym", + "val" : "girdle plus limb or fin", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "pred" : "hasRelatedSynonym", + "val" : "limb", + "xrefs" : [ "FMA:7182" ] } ], "xrefs" : [ { - "val" : "EMAPA:35932" + "val" : "EMAPA:37858" }, { - "val" : "FMA:86188" + "val" : "FMA:7182" }, { - "val" : "MA:0000066" + "val" : "VSAO:0000214" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "It is still called a complex when one of the two parts is missing (?) 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There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-04-23T10:46:51Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004087", - "lbl" : "vena cava", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010709", + "lbl" : "pelvic complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.", - "xrefs" : [ "Wikipedia:Venae_cavae", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.", + "xrefs" : [ "VSAO:0000215" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "caval vein" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "venae cavae", - "xrefs" : [ "Wikipedia:Venae_cavae" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010215" - }, { - "val" : "BTO:0001438" - }, { - "val" : "EMAPA:18415" + "pred" : "hasExactSynonym", + "val" : "pelvic appendage/girdle complex", + "xrefs" : [ "VSAO:0000215" ] }, { - "val" : "FMA:321896" + "pred" : "hasExactSynonym", + "val" : "pelvic girdle plus pelvic limb or fin", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "GAID:547" + "pred" : "hasExactSynonym", + "val" : "pelvic girdle plus posterior limb or fin", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "MA:0000068" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "pred" : "hasRelatedSynonym", + "val" : "lower limb", + "xrefs" : [ "FMA:7184" ] }, { - "val" : "MESH:D014684" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "pred" : "hasRelatedSynonym", + "val" : "lower limb and pelvic girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "NCIT:C12817" + "pred" : "hasRelatedSynonym", + "val" : "lower limb and pelvis", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37863" }, { - "val" : "SCTID:244405007" + "val" : "FMA:7184" }, { - "val" : "UMLS:C0042460" + "val" : "SCTID:416631005" }, { - "val" : "Wikipedia:Venae_cavae" + "val" : "VSAO:0000215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004100", - "lbl" : "renal collecting system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010719", + "lbl" : "girdle skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. 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"val" : "galen:GenitoUrinarySystem" + "val" : "VSAO:0000306" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004134", - "lbl" : "proximal tubule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011585", + "lbl" : "cell condensation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].", - "xrefs" : [ "GO:0072014" ] + "val" : "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000006", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "kidney proximal tubule", - "xrefs" : [ "MA:0002611" ] - }, { - "pred" : "hasExactSynonym", - "val" : "proximal kidney tubule", - "xrefs" : [ "MESH:A05.810.453.736.560.570" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal proximal tubule" - } ], "xrefs" : [ { - "val" : "BTO:0001498" - }, { - "val" : "CALOHA:TS-0509" - }, { - "val" : "EMAPA:28281" - }, { - "val" : "MA:0002611" + "val" : "VSAO:0000006" }, { - "val" : "MESH:D007687" + "val" : "XAO:0004021" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - ensure definition works across species." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "consider obsoleting, coordinate with VSAO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004135", - "lbl" : "distal tubule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011676", + "lbl" : "subdivision of organism along main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments.", - "xrefs" : [ "GO:0072017" ] + "val" : "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "kidney distal tubule", - "xrefs" : [ "MA:0002633" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal distal tubule" - } ], - "xrefs" : [ { - "val" : "BTO:0000482" - }, { - "val" : "CALOHA:TS-0504" - }, { - "val" : "EMAPA:28387" + "val" : "axial subdivision of organism" }, { - "val" : "MA:0002633" + "pred" : "hasRelatedSynonym", + "val" : "body segment" }, { - "val" : "MESH:D007686" + "pred" : "hasRelatedSynonym", + "val" : "main body segment" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004136", - "lbl" : "intermediate tubule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", + "lbl" : "embryonic cardiovascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules.", - "xrefs" : [ "GO:0072018" ] + "val" : "A cardiovascular system that is part of a conceptus.", + "xrefs" : [ "OBOL:automatic" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "renal intermediate tubule" + "val" : "conceptus cardiovascular system" }, { - "pred" : "hasExactSynonym", - "val" : "tubulus attenuatus", - "xrefs" : [ "FMA:17718" ] + "pred" : "hasRelatedSynonym", + "val" : "embryonic circulatory system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fetal circulatory system" } ], "xrefs" : [ { - "val" : "FMA:17718" + "val" : "EHDAA2:0000216" + }, { + "val" : "FMA:305965" + }, { + "val" : "NCIT:C34148" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check for applicability across species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", - "lbl" : "cardiogenic plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", + "lbl" : "coelom", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The first recognizable structure derived from the heart field.", - "xrefs" : [ "GO:0003142" ] + "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "myocardial plate", - "xrefs" : [ "EHDAA2:0000215" ] + "pred" : "hasNarrowSynonym", + "val" : "enterocoelom", + "xrefs" : [ "NCBITaxon:33511" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac crescent", - "xrefs" : [ "EMAPA:16106" ] + "pred" : "hasNarrowSynonym", + "val" : "haemocoelom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "schizocoelom" }, { "pred" : "hasRelatedSynonym", - "val" : "cardiogenic crescent", - "xrefs" : [ "GO:0003142" ] + "val" : "coelem" }, { "pred" : "hasRelatedSynonym", - "val" : "heart rudiment" + "val" : "coelomic cavity", + "xrefs" : [ "EHDAA2:0004731" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0000215" - }, { - "val" : "EMAPA:16106" + "val" : "EHDAA2:0004731" }, { - "val" : "VHOG:0000975" + "val" : "Wikipedia:Coelom" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" + "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", - "lbl" : "primary heart field", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012274", + "lbl" : "columnar epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", - "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] + "val" : "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].", + "xrefs" : [ "Wikipedia:Columnar_epithelium" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "first heart field", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primary heart field", - "xrefs" : [ "PMID:17276708", "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "FHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "PHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "heart field", - "xrefs" : [ "XAO:0004185" ] - } ], "xrefs" : [ { - "val" : "XAO:0004185" + "val" : "Wikipedia:Columnar_epithelium" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27727,42 +28018,23 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", - "lbl" : "heart tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", + "lbl" : "meso-epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelial tube that will give rise to the mature heart.", - "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] + "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "embryonic heart tube", - "xrefs" : [ "GO:0003143" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial heart tube", - "xrefs" : [ "MP:0012700" ] + "val" : "mesoderm-derived epithelium" }, { "pred" : "hasExactSynonym", - "val" : "endocardial tube", - "xrefs" : [ "XAO:0000337" ] + "val" : "mesoepithelium" } ], "xrefs" : [ { - "val" : "AAO:0010411" - }, { - "val" : "EFO:0003526" - }, { - "val" : "EMAPA:32685" - }, { - "val" : "NCIT:C34161" - }, { - "val" : "TAO:0000360" - }, { - "val" : "XAO:0000337" - }, { - "val" : "ZFA:0000360" + "val" : "FMA:86452" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27770,26 +28042,22 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", - "lbl" : "cardiac chamber", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012292", + "lbl" : "embryonic cloacal fold", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", - "xrefs" : [ "GO:0003205" ] + "val" : "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly.", + "xrefs" : [ "MP:0011836", "MP:anna" ] }, - "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], + "comments" : [ "We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chamber of heart" - }, { - "pred" : "hasExactSynonym", - "val" : "heart chamber" + "pred" : "hasBroadSynonym", + "val" : "cloacal fold", + "xrefs" : [ "EHDAA2:0004009" ] } ], "xrefs" : [ { - "val" : "FMA:7095" - }, { - "val" : "SCTID:276456008" + "val" : "EHDAA2:0004009" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27797,30 +28065,68 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004176", - "lbl" : "external genitalia", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012361", + "lbl" : "internal anal region", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EHDAA2:0004588" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0012469", + "lbl" : "external anal region", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EHDAA2:0004589" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0012476", + "lbl" : "skeleton of pelvic complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The external genitalia are the outer sex organs, such as the penis or vulva in mammals.", - "xrefs" : [ "GO:0035261" ] + "val" : "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "external genitalia" + "pred" : "hasRelatedSynonym", + "val" : "bones of lower limb", + "xrefs" : [ "FMA:24140" ] }, { "pred" : "hasRelatedSynonym", - "val" : "external reproductive organ" + "val" : "lower limb skeleton", + "xrefs" : [ "FMA:24140" ] }, { "pred" : "hasRelatedSynonym", - "val" : "external sex organ" + "val" : "ossa membri inferioris", + "xrefs" : [ "FMA:TA" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "pelvic complex skeleton", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of bones of lower limb", + "xrefs" : [ "FMA:24140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "skeleton of posterior limb/fin and girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { - "val" : "FMA:45643" - }, { - "val" : "SCTID:362207005" + "val" : "FMA:24140" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27828,109 +28134,117 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004188", - "lbl" : "glomerular epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013241", + "lbl" : "embryonic urethral groove", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.", - "xrefs" : [ "GO:0072010" ] + "val" : "The precursor of the urethra.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "epithelium of glomerulus" - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of kidney glomerulus" + "val" : "sulcus urethralis primarius", + "xrefs" : [ "Wikipedia:Urethral_groove" ] }, { "pred" : "hasExactSynonym", - "val" : "epithelium of renal glomerulus" + "val" : "urethral groove" }, { "pred" : "hasExactSynonym", - "val" : "kidney glomerular epithelium", - "xrefs" : [ "MA:0002847" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "glomerular epithelial cell", - "xrefs" : [ "BTO:0001515" ] + "val" : "urethral sulcus" } ], "xrefs" : [ { - "val" : "BTO:0001515" - }, { - "val" : "EMAPA:35458" + "val" : "SCTID:361531004" }, { - "val" : "MA:0002847" + "val" : "Wikipedia:Urethral_groove" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check - GO says outer, BTO says inner. Make this a superclass" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004190", - "lbl" : "renal glomerulus vasculature", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", + "lbl" : "subdivision of tube", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013686", + "lbl" : "anatomical conduit space", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.", - "xrefs" : [ "GO:0072012" ] + "val" : "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].", + "xrefs" : [ "FMA:9338", "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "glomerulus vasculature", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus vascular network", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus vasculature", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "vascular network of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "vasculature of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasNarrowSynonym", + "val" : "foramen space" + } ], + "xrefs" : [ { + "val" : "FMA:9338" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004198", - "lbl" : "comma-shaped body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", + "lbl" : "main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron.", - "xrefs" : [ "GO:0072049" ] + "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", + "lbl" : "body proper", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The region of the organism associated with the visceral organs.", + "xrefs" : [ "AEO:0000103" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "CSB" + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] } ], "xrefs" : [ { - "val" : "EMAPA:27681" + "val" : "AEO:0000103" }, { - "val" : "ZFA:0005588" + "val" : "BTO:0001489" + }, { + "val" : "FMA:231424" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27938,183 +28252,92 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004199", - "lbl" : "S-shaped body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013756", + "lbl" : "venous blood", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.", - "xrefs" : [ "GO:0072050" ] + "val" : "A blood that is part of a vein.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasExactSynonym", - "val" : "SSB" + "val" : "blood in vein", + "xrefs" : [ "FMA:83067" ] }, { "pred" : "hasExactSynonym", - "val" : "stage II nephron", - "xrefs" : [ "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] + "val" : "portion of venous blood", + "xrefs" : [ "FMA:83067" ] + }, { + "pred" : "hasExactSynonym", + "val" : "venous blood", + "xrefs" : [ "FMA:83067" ] } ], "xrefs" : [ { - "val" : "EMAPA:27756" - }, { - "val" : "ZFA:0005589" + "val" : "FMA:83067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004200", - "lbl" : "kidney pyramid", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013768", + "lbl" : "great vessel of heart", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.", - "xrefs" : [ "GO:0072056", "http://anatomy.uams.edu/anatomyhtml/kidney.html" ] + "val" : "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.", + "xrefs" : [ "Wikipedia:Great_vessels" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "Groupings may vary - typically pulmonary vessels and aorta and vena cavae" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { "pred" : "hasBroadSynonym", - "val" : "pyramid", - "xrefs" : [ "GO:0072056" ] - }, { - "pred" : "hasExactSynonym", - "val" : "Malpighian pyramid", - "xrefs" : [ "Wikipedia:Renal_pyramids" ] + "val" : "great vessel" }, { "pred" : "hasExactSynonym", - "val" : "renal pyramid", - "xrefs" : [ "Wikipedia:Renal_pyramids" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", - "pred" : "hasRelatedSynonym", - "val" : "Malphigian pyramid", - "xrefs" : [ "BTO:0003926" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Malpighian pyramid" - }, { - "pred" : "hasRelatedSynonym", - "val" : "medullary pyramid" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", - "pred" : "hasRelatedSynonym", - "val" : "pyramid of Malphigi", - "xrefs" : [ "ncithesaurus:Pyramid_of_Malpighi" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pyramid of Malpighi", - "xrefs" : [ "UBERON:cjm" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "pyramides renales", - "xrefs" : [ "Wikipedia:Renal_pyramids" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pyramis renalis", - "xrefs" : [ "BTO:0003926" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "renal medullary region", - "xrefs" : [ "FMA:258870" ] + "val" : "great vessel of thorax" } ], - "xrefs" : [ { - "val" : "BTO:0003926" - }, { - "val" : "FMA:258870" - }, { - "val" : "MA:0001654" - }, { - "val" : "NCIT:C12886" - }, { - "val" : "NCIT:C33436" - }, { - "val" : "SCTID:361328001" - }, { - "val" : "UMLS:C0227629" + "xrefs" : [ { + "val" : "EMAPA:36460" }, { - "val" : "UMLS:C1514613" + "val" : "SCTID:304066000" }, { - "val" : "Wikipedia:Renal_pyramids" + "val" : "Wikipedia:Great_vessels" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0002449" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005098" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004202", - "lbl" : "kidney outer medulla outer stripe", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", + "lbl" : "thoracic skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules.", - "xrefs" : [ "GO:0072058" ] + "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", + "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "outer medulla outer stripe", - "xrefs" : [ "MA:0002629" ] - }, { - "pred" : "hasExactSynonym", - "val" : "outer stripe", - "xrefs" : [ "GO:0072058" ] - }, { - "pred" : "hasExactSynonym", - "val" : "outer stripe of medulla of kidney", - "xrefs" : [ "FMA:76662" ] - }, { - "pred" : "hasExactSynonym", - "val" : "outer stripe of outer medulla", - "xrefs" : [ "EMAPA:29663" ] + "val" : "skeleton of thorax" }, { "pred" : "hasExactSynonym", - "val" : "outer stripe of renal medulla", - "xrefs" : [ "FMA:76662" ] + "val" : "thoracic part of axial skeleton" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "stria externa medullae renalis", - "xrefs" : [ "FMA:76662", "FMA:TA" ] + "val" : "thoracic skeleton", + "xrefs" : [ "EHDAA2:0002013" ] } ], "xrefs" : [ { - "val" : "EMAPA:29663" + "val" : "EHDAA2:0002013" }, { - "val" : "FMA:76662" + "val" : "FMA:77169" }, { - "val" : "MA:0002629" + "val" : "Wikipedia:Thoracic_skeleton" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -28125,23 +28348,20 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004208", - "lbl" : "nephrogenic mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", + "lbl" : "primordial vasculature", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron.", - "xrefs" : [ "GO:0072076" ] + "val" : "A portion of tissue that will develop into vasculature.", + "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] }, - "comments" : [ "The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of nephron", - "xrefs" : [ "OBOL:automatic" ] + "xrefs" : [ { + "val" : "EFO:0003708" }, { - "pred" : "hasExactSynonym", - "val" : "nephron mesenchyme", - "xrefs" : [ "OBOL:automatic" ] + "val" : "TAO:0005076" + }, { + "val" : "ZFA:0005076" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28149,48 +28369,45 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004209", - "lbl" : "renal vesicle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", + "lbl" : "lateral structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.", - "xrefs" : [ "GO:0072077" ] + "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "stage I nephron", - "xrefs" : [ "ZFA:0005586", "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004211", - "lbl" : "nephron epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", + "lbl" : "circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The nephron epithelium is a tissue that covers the surface of a nephron.", - "xrefs" : [ "GO:0072088" ] + "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial tissue of nephron", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasBroadSynonym", + "val" : "heart" }, { "pred" : "hasExactSynonym", - "val" : "epithelium of nephron", - "xrefs" : [ "OBOL:automatic" ] + "val" : "cardiac pump" }, { "pred" : "hasExactSynonym", - "val" : "nephron epithelial tissue", - "xrefs" : [ "OBOL:automatic" ] + "val" : "heart or heart like organ" + }, { + "pred" : "hasNarrowSynonym", + "val" : "circulatory vessel" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardiac structure" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28198,64 +28415,20 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004212", - "lbl" : "glomerular capillary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", + "lbl" : "heart plus pericardium", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus.", - "xrefs" : [ "MGI:csmith", "MP:0011320" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood capillary of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary vessel of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus blood capillary", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus capillary", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus capillary vessel", - "xrefs" : [ "OBOL:automatic" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "glomerular capillaries" - }, { - "pred" : "hasRelatedSynonym", - "val" : "glomerular capillary system", - "xrefs" : [ "MA:0002587" ] + "val" : "heart/pericardium", + "xrefs" : [ "MA:0002449" ] } ], "xrefs" : [ { - "val" : "EMAPA:28245" - }, { - "val" : "FMA:274259" - }, { - "val" : "MA:0002587" - }, { - "val" : "NCIT:C32684" - }, { - "val" : "SCTID:362049007" - }, { - "val" : "TAO:0005284" - }, { - "val" : "UMLS:C0226356" + "val" : "EMAPA:37597" }, { - "val" : "ZFA:0005284" + "val" : "MA:0002449" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -28266,86 +28439,95 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016566", + "lbl" : "pit", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "An roughly circular indentation in a surface.", + "xrefs" : [ "AEO:0000204", "AEO:JB" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "AEO:0000204" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", + "lbl" : "future central nervous system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Primordium that develops into the central nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "set of all bones" + "val" : "future CNS" }, { "pred" : "hasExactSynonym", - "val" : "set of bones of body" + "val" : "presumptive central nervous system" } ], - "xrefs" : [ { - "val" : "AEO:0000168" - }, { - "val" : "EHDAA2:0001843" - }, { - "val" : "EHDAA:5047" - }, { - "val" : "EMAPA:17213" - }, { - "val" : "FMA:23875" - }, { - "val" : "GAID:177" - }, { - "val" : "MA:0003006" - }, { - "val" : "MAT:0000032" - }, { - "val" : "MESH:D012863" - }, { - "val" : "MIAA:0000032" - }, { - "val" : "SCTID:361378004" - }, { - "val" : "VSAO:0000026" - }, { - "val" : "Wikipedia:Skeleton" - }, { - "val" : "XAO:0004053" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000469" }, { - "val" : "galen:Skeleton" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", + "lbl" : "future nervous system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Primordium that develops into the nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "presumptive nervous system", + "xrefs" : [ "AAO:0000477" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000477" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" } ] } }, { - 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The heart rudiment is the first structure of the heart tube.", - "xrefs" : [ "GO:0003313" ] + "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", + "xrefs" : [ "AEO:0000195", "AEO:JB" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "heart cone", - "xrefs" : [ "GO:0003313" ] + "val" : "extra-embryonic component" }, { "pred" : "hasExactSynonym", - "val" : "rudimentary heart", - "xrefs" : [ "ZFA:0000115" ] + "val" : "extraembryonic component", + "xrefs" : [ "AEO:0000195" ] } ], "xrefs" : [ { - "val" : "TAO:0000115" + "val" : "AEO:0000195" }, { - "val" : "ZFA:0000115" + "val" : "EHDAA2:0000003" + }, { + "val" : "EMAPA:16042" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28353,4530 +28535,3603 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004341", - "lbl" : "primitive streak", + "id" : "http://purl.obolibrary.org/obo/UBERON_0018707", + "lbl" : "bladder organ", "type" : "CLASS", "meta" : { "definition" : { - 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The renal pelvis is the large cavity in the middle of each kidney. 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Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.", + "xrefs" : [ "Wikipedia:Microcirculation", "http://orcid.org/0000-0002-7073-9172" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "microvasculature" }, { - "val" : "galen:SkeletalStructure" + "pred" : "hasBroadSynonym", + "val" : "microvessel" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-2825-0621" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", + "id" : "http://purl.obolibrary.org/obo/UBERON_8450002", + "lbl" : "excretory system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] + "val" : "An anatomical system that eliminates waste products that arise as a result of metabolic activity.", + "xrefs" : [ "GO:0007588" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "MA:0003007" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-6095-8718" }, { - "val" : "SCTID:361827000" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-05-25T18:21:29Z" }, { - "val" : "VSAO:0000181" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004810", - "lbl" : "nephron tubule epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", + "lbl" : "visceral muscle tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The cellular avascular layer of the renal tubule luminar surfaces.", - "xrefs" : [ "MGI:csmith", "MP:0009640" ] + "val" : "A muscle tissue that is associated with soft internal organs (viscera).", + "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; 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Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of kidney", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. 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A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "pred" : "hasRelatedSynonym", - "val" : "renal epithelium", - "xrefs" : [ "EMAPA:35457" ] - } ], - "xrefs" : [ { - "val" : "BTO:0000059" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "CALOHA:TS-0505" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "EMAPA:35457" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "MA:0002846" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", - "lbl" : "cardiovascular system endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that is part of the cardiovascular system.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a core relation that holds between a whole and its part" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "endothelia", - "xrefs" : [ "ZFA:0001639" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "vascular endothelia", - "xrefs" : [ "XAO:0000356" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BTO:0001853" - }, { - "val" : "EMAPA:35201" - }, { - "val" : "GAID:519" - }, { - "val" : "MA:0000717" - }, { - "val" : "MESH:D004730" - }, { - "val" : "NCIT:C13053" + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { - "val" : "TAO:0002171" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "UMLS:C0014261" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "val" : "VHOG:0001217" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "XAO:0000356" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "ZFA:0001639" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'endothelium'" + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004872", - "lbl" : "splanchnic layer of lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "visceral mesoderm", - "xrefs" : [ "BILA:0000044", "http://www.drugs.com/dict/visceral-mesoderm.html", "http://www.stedmans.com/" ] - }, { - "pred" : "hasExactSynonym", - "val" : "inner layer of lateral plate mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011102" - }, { - "val" : "BILA:0000044" - }, { - "val" : "FMA:295568" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" - }, { - "val" : "XAO:0000276" + "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004874", - "lbl" : "somatopleure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].", - "xrefs" : [ "Wikipedia:Somatopleure" ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EHDAA2:0001847" - }, { - "val" : "EHDAA:381" - }, { - "val" : "EMAPA:16180" - }, { - "val" : "FMA:295566" - }, { - "val" : "NCIT:C34301" - }, { - "val" : "UMLS:C1519423" - }, { - "val" : "VHOG:0000557" - }, { - "val" : "Wikipedia:Somatopleure" + "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004875", - "lbl" : "nephrogenic cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A portion of the urogenital ridge which is the source of much of the urinary system[WP].", - "xrefs" : [ "Wikipedia:Nephrogenic_cord" ] + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "part_of or develops_from urogenital ridge?" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "chorda nephrogenica", - "xrefs" : [ "Wikipedia:Nephrogenic_cord" ] - } ], + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "xrefs" : [ { - "val" : "FMA:72168" - }, { - "val" : "NCIT:C34219" - }, { - "val" : "SCTID:361405003" - }, { - "val" : "UMLS:C1283944" - }, { - "val" : "Wikipedia:Nephrogenic_cord" + "val" : "GOREL:0002003" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004876", - "lbl" : "urogenital fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].", - "xrefs" : [ "MP:0011835", "MP:anna", "Wikipedia:Urogenital_folds" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "urethral fold", - "xrefs" : [ "EMAPA:30888" ] - }, { - "pred" : "hasExactSynonym", - "val" : "urogenital fold", - "xrefs" : [ "EHDAA2:0004022", "MP:0011835" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", - "pred" : "hasRelatedSynonym", - "val" : "urogenital ridge", - "xrefs" : [ "MP:0011835" ] - } ], "xrefs" : [ { - "val" : "EHDAA2:0004022" - }, { - "val" : "EMAPA:30888" - }, { - "val" : "FMA:321919" - }, { - "val" : "Wikipedia:Urogenital_folds" + "val" : "GOREL:0002004" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], "xrefs" : [ { - "val" : "AAO:0000478" - }, { - "val" : "EFO:0003426" - }, { - "val" : "TAO:0000091" - }, { - "val" : "ZFA:0000091" + "val" : "RO:0000053" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004905", - "lbl" : "articulation", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], "xrefs" : [ { - "val" : "FBbt:00005811" + "val" : "RO:0000056" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A proximal-distal subdivision of the digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system subdivision", - "xrefs" : [ "FMA:71131" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut section", - "xrefs" : [ "FBbt:00100315" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "segment of intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "subdivision of alimentary system", - "xrefs" : [ "FMA:71131" ] - } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { - "val" : "FMA:71131" + "val" : "RO:0000057" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "lbl" : "organ component layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A part of a wall of an organ that forms a layer.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FMA:82485" - } ], + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005061", - "lbl" : "neural groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.", - "xrefs" : [ "GO:0001842", "Wikipedia:Neural_groove", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "xrefs" : [ { - "val" : "AAO:0011071" - }, { - "val" : "EMAPA:35594" - }, { - "val" : "FMA:295624" - }, { - "val" : "NCIT:C34224" - }, { - "val" : "SCTID:361463007" - }, { - "val" : "UMLS:C0814992" - }, { - "val" : "Wikipedia:Neural_groove" - }, { - "val" : "XAO:0000248" - }, { - "val" : "neuronames:1363" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "lbl" : "neural fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "One of the two elevated edges of the neural groove[GO,MP].", - "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "medullary fold", - "xrefs" : [ "MP:0011256" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001249" - }, { - "val" : "FMA:295618" - }, { - "val" : "NCIT:C34223" - }, { - "val" : "SCTID:361461009" - }, { - "val" : "UMLS:C0814993" - }, { - "val" : "Wikipedia:Neural_fold" - }, { - "val" : "XAO:0004087" - }, { - "val" : "neuronames:1364" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005068", - "lbl" : "neural rod", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].", - "xrefs" : [ "GO:0014024", "ZFA:0000133" ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural tube rod", - "xrefs" : [ "GO:0014027" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003498" - }, { - "val" : "TAO:0000133" - }, { - "val" : "ZFA:0000133" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005080", - "lbl" : "metanephric ureteric bud", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].", - "xrefs" : [ "GO:0035502" ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005081", - "lbl" : "ureter ureteric bud", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].", - "xrefs" : [ "GO:0035503" ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "lbl" : "muscle structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", - "xrefs" : [ "GO:0061061" ] + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "musculus", - "xrefs" : [ "FMA:30316" ] + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle element" - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "FMA:30316" + "val" : "RO:0002007" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005095", - "lbl" : "kidney rudiment", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Missing definition for term UBERON:0005095. Please replace it using linked reference.", - "xrefs" : [ "GO:0072003" ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "kidney anlage", - "xrefs" : [ "GOC:mtg_kidney_jan10" ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "class added for consistency with GO - consider merging with kidney mesenchyme." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005096", - "lbl" : "descending thin limb", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO].", - "xrefs" : [ "GO:0072022", "Wikipedia:Descending_limb_of_loop_of_Henle" ] + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "descending thin limb of loop of Henle" - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle descending thin limb" - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle thin descending limb", - "xrefs" : [ "MA:0002625" ] - }, { - "pred" : "hasExactSynonym", - "val" : "pars descendens (tubulus attenuatus)", - "xrefs" : [ "FMA:17719" ] - }, { - "pred" : "hasExactSynonym", - "val" : "thin descending limb" - }, { - "pred" : "hasRelatedSynonym", - "val" : "descending limb of Henle's loop", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "descending limb of loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "thin descending limb of loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "thin descending limb of the loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "thin descending loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - } ], + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "xrefs" : [ { - "val" : "EMAPA:35514" - }, { - "val" : "FMA:17719" - }, { - "val" : "MA:0002625" - }, { - "val" : "Wikipedia:Descending_limb_of_loop_of_Henle" + "val" : "RO:0002087" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2276" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005097", - "lbl" : "renal connecting tubule", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO].", - "xrefs" : [ "GO:0072027", "Wikipedia:Connecting_tubule" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "connecting tubule", - "xrefs" : [ "MA:0002610" ] - }, { - "pred" : "hasExactSynonym", - "val" : "kidney connecting tubule", - "xrefs" : [ "MA:0002610" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tubulus renalis arcuatus", - "xrefs" : [ "Wikipedia:Connecting_tubule" ] - } ], + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BTO:0004539" - }, { - "val" : "EMAPA:27758" - }, { - "val" : "EMAPA:27790" - }, { - "val" : "EMAPA:28011" - }, { - "val" : "MA:0002610" - }, { - "val" : "Wikipedia:Connecting_tubule" + "val" : "RO:0002090" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005103", - "lbl" : "mesonephric epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelium that is part of a mesonephros [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005156", - "lbl" : "reproductive structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any anatomical structure that is part of the reproductive system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "reproductive system element" - }, { - "pred" : "hasExactSynonym", - "val" : "reproductive system structure" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", - "lbl" : "epithelial fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelial sheet bent on a linear axis.", - "xrefs" : [ "GO:0060571" ] + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005164", - "lbl" : "ascending limb of loop of Henle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP].", - "xrefs" : [ "MP:0011342", "Wikipedia:Ascending_limb_of_loop_of_Henle" ] + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ascending limb" - }, { - "pred" : "hasExactSynonym", - "val" : "ascending limb of Henle's loop" - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle ascending limb", - "xrefs" : [ "MP:0011342" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "distal straight tubule" - } ], - "xrefs" : [ { - "val" : "EMAPA:35510" - }, { - "val" : "FMA:17717" - }, { - "val" : "MA:0001676" - }, { - "val" : "NCIT:C32154" - }, { - "val" : "SCTID:245434005" - }, { - "val" : "UMLS:C0227658" - }, { - "val" : "Wikipedia:Ascending_limb_of_loop_of_Henle" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005167", - "lbl" : "papillary duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "lbl" : "has postsynaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx.", - "xrefs" : [ "http://encyclopedia.thefreedictionary.com/" ] + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "papillary duct" - }, { - "pred" : "hasExactSynonym", - "val" : "papillary duct of kidney" - }, { - "pred" : "hasExactSynonym", - "val" : "renal papillary duct" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bellini's duct", - "xrefs" : [ "MP:0011331" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "duct of Bellini" - } ], - "xrefs" : [ { - "val" : "BTO:0004540" - }, { - "val" : "EMAPA:35655" - }, { - "val" : "MA:0001646" - }, { - "val" : "SCTID:110623009" - }, { - "val" : "Wikipedia:Duct_of_Bellini" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005169", - "lbl" : "interstitial tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002113", + "lbl" : "has presynaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Connective tissue between the cellular elements of a structure.", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/tissue" ] + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "interstitium" - } ], - "xrefs" : [ { - "val" : "FMA:86301" - }, { - "val" : "SCTID:85293002" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "specify differentia from stroma" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005172", - "lbl" : "abdomen element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "abdomen organ", - "xrefs" : [ "MA:0000522" ] - } ], - "xrefs" : [ { - "val" : "MA:0000522" - }, { - "val" : "SCTID:272631008" - } ], + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005173", - "lbl" : "abdominal segment element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "abdominal segment organ", - "xrefs" : [ "MA:0000529" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37062" - }, { - "val" : "MA:0000529" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", - "lbl" : "trunk region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trunk organ", - "xrefs" : [ "MA:0000516" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "EMAPA:37270" - }, { - "val" : "MA:0000516" + "val" : "RO:0002131" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "overlaps" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005178", - "lbl" : "thoracic cavity element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracic cavity organ", - "xrefs" : [ "MA:0000557" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37273" - }, { - "val" : "MA:0000557" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that ( some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005179", - "lbl" : "pelvic region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pelvic element" - }, { - "pred" : "hasExactSynonym", - "val" : "pelvis organ", - "xrefs" : [ "MA:0000543" ] - }, { - "pred" : "hasExactSynonym", - "val" : "pelvis region organ" - } ], - "xrefs" : [ { - "val" : "EMAPA:37275" - }, { - "val" : "MA:0000543" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", - "lbl" : "thoracic segment organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "upper body organ", - "xrefs" : [ "MA:0000563" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37271" - }, { - "val" : "MA:0000563" - } ], + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005185", - "lbl" : "renal medulla collecting duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The portion of the collecting duct that resides in the renal medulla.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "kidney medulla collecting duct", - "xrefs" : [ "MA:0002935" ] - }, { - "pred" : "hasExactSynonym", - "val" : "medullary collecting duct", - "xrefs" : [ "EMAPA:28061" ] - } ], - "xrefs" : [ { - "val" : "BTO:0004536" - }, { - "val" : "EMAPA:28061" + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " }, { - "val" : "EMAPA:35459" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { - "val" : "MA:0002935" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005215", - "lbl" : "kidney interstitium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.", - "xrefs" : [ "DOI:10.1038/ki.1991.49", "PMID:18575881", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "interstitial tissue of kidney" - }, { - "pred" : "hasExactSynonym", - "val" : "renal interstitial tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "renal interstitium", - "xrefs" : [ "FMA:70983" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal stroma", - "xrefs" : [ "FMA:70983" ] - }, { - "pred" : "hasExactSynonym", - "val" : "stroma of kidney", - "xrefs" : [ "FMA:70983" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "kidney interstitium group", - "xrefs" : [ "EMAPA:28518" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:28518" - }, { - "val" : "FMA:70983" - }, { - "val" : "MA:0002616" - }, { - "val" : "NCIT:C33459" - }, { - "val" : "SCTID:362210003" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005256", - "lbl" : "trunk mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Mesenchyme that is part of a developing trunk.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "trunk and cervical mesenchyme", - "xrefs" : [ "EHDAA2:0002092" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003485" - }, { - "val" : "EHDAA2:0002092" - }, { - "val" : "EHDAA:377" - }, { - "val" : "EMAPA:16177" - }, { - "val" : "TAO:0000081" - }, { - "val" : "VHOG:0000281" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "val" : "ZFA:0000081" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005291", - "lbl" : "embryonic tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A portion of tissue that is part of an embryo.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of embryonic tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing tissue" - } ], - "xrefs" : [ { - "val" : "CALOHA:TS-2100" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005423", - "lbl" : "developing anatomical structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "developing structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "developmental structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "developmental tissue", - "xrefs" : [ "MIAA:0000019" ] - } ], + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AEO:0000125" - }, { - "val" : "CALOHA:TS-2122" - }, { - "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" - }, { - "val" : "FMA:292313" - }, { - "val" : "MIAA:0000019" + "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005498", - "lbl" : "primitive heart tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Multi-tissue structure that arises from the heart rudiment and will become the heart tube.", - "xrefs" : [ "ZFA:0000149" ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive heart tube", - "xrefs" : [ "EMAPA:16215" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "early primitive heart tube", - "xrefs" : [ "EMAPA:16208" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001512" - }, { - "val" : "EHDAA:424" - }, { - "val" : "EHDAA:436" - }, { - "val" : "EMAPA:16215" - }, { - "val" : "FMA:321916" - }, { - "val" : "SCTID:361522004" - }, { - "val" : "TAO:0000149" - }, { - "val" : "Wikipedia:Primitive_heart_tube" - }, { - "val" : "ZFA:0000149" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005564", - "lbl" : "gonad primordium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Portion of tissue that gives rise to the immature gonad.", - "xrefs" : [ "ZFA:0001262" ] + "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future gonad", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "gonadal primordium", - "xrefs" : [ "ZFA:0001262" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primitive gonad", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "undifferentiated gonad", - "xrefs" : [ "ZFA:0001262" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "immature gonad", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003651" - }, { - "val" : "EHDAA:5927" - }, { - "val" : "EMAPA:17204" - }, { - "val" : "RETIRED_EHDAA2:0002148" - }, { - "val" : "TAO:0001262" - }, { - "val" : "WBbt:0008366" - }, { - "val" : "ZFA:0001262" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005721", - "lbl" : "pronephric mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A mesoderm that has the potential to develop into a pronephros.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, - "comments" : [ "the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 \"Developmental Biology\", PMID:10720431 \"Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm\"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "pronephric anlage", - "xrefs" : [ "XAO:0000264" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pronephric bulge", - "xrefs" : [ "XAO:0000264" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pronephric mesenchyme", - "xrefs" : [ "XAO:0000264" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pronephric primordium", - "xrefs" : [ "XAO:0000264" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011090" - }, { - "val" : "EFO:0003479" - }, { - "val" : "TAO:0000067" - }, { - "val" : "VHOG:0001239" - }, { - "val" : "XAO:0000264" - }, { - "val" : "ZFA:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005749", - "lbl" : "glomerular tuft", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The capillary loops of the kidney that normally function as a filtration unit[MP].", - "xrefs" : [ "MP:0005325", "Wikipedia:Glomerulus", "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "glomerular capillary tuft" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", - "pred" : "hasRelatedSynonym", - "val" : "glomerulus", - "xrefs" : [ "EMAPA:28239" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:28239" - }, { - "val" : "Wikipedia:Glomerulus" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005753", - "lbl" : "caudal part of nephrogenic cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.", - "xrefs" : [ "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "caudal portion of nephrogenic cord", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "caudal region of nephrogenic cord", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rear part of nephrogenic cord", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rear portion of nephrogenic cord", - "xrefs" : [ "Wikipedia:Metanephros#Metanephros" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005754", - "lbl" : "rostral part of nephrogenic cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.", - "xrefs" : [ "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005764", - "lbl" : "acellular membrane", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An acellular anatomical structure that is the bounding layer of a anatomical structure.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "FMA:63871" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "lbl" : "basement membrane of epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.", - "xrefs" : [ "Wikipedia:Basement_membrane", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. 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"id" : "http://purl.obolibrary.org/obo/UBERON_0007798", - "lbl" : "vascular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all blood and lymph vessels.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "BTO:0001085" - }, { - "val" : "CALOHA:TS-2053" - 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It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007823", - "lbl" : "appendage girdle region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).", - "xrefs" : [ "UBERONREF:0000003", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "girdle" - }, { - "pred" : "hasBroadSynonym", - "val" : "girdle region" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "fin girdle" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "fin girdle region" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "limb girdle" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "limb girdle region" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:37854" - }, { - "val" : "FMA:24874" - }, { - "val" : "VSAO:0000303" + "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007824" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007832", - "lbl" : "pelvic girdle skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.", - "xrefs" : [ "VSAO:0000155", "Wikipedia:Pelvis" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pelvic girdle skeleton", - "xrefs" : [ "VSAO:0000155" ] - }, { - "pred" : "hasExactSynonym", - "val" : "skeletal parts of pelvic girdle", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "skeleton of pelvic girdle", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", "pred" : "hasRelatedSynonym", - "val" : "pelvic girdle", - "xrefs" : [ "VSAO:0000155" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "AAO:0000426" - }, { - "val" : "AAO:0000768" - }, { - "val" : "EFO:0000947" - }, { - "val" : "EHDAA2:0001426" - }, { - "val" : "EHDAA:7149" - }, { - "val" : "EHDAA:8324" - }, { - "val" : "EMAPA:18028" - }, { - "val" : "FMA:87592" - }, { - "val" : "MAT:0000182" - }, { - "val" : "MIAA:0000182" - }, { - "val" : "TAO:0000565" - }, { - "val" : "VHOG:0000305" - }, { - "val" : "VSAO:0000155" - }, { - "val" : "Wikipedia:Pelvis" - }, { - "val" : "XAO:0003064" - }, { - "val" : "ZFA:0000565" - }, { - "val" : "galen:PelvicGirdle" - }, { - "val" : "http://people.eku.edu/ritchisong/pectoralgirdles.gif" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0008987", - "lbl" : "renal parenchyma", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The functional tissue of the kidney, consisting of the nephrons.", - "xrefs" : [ "BTO:0003604" ] + "val" : "inverse of causally upstream of or within" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "parenchyma of kidney", - "xrefs" : [ "FMA:15574" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "kidney parenchyma", - "xrefs" : [ "BTO:0003604" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "xrefs" : [ { - "val" : "BTO:0003604" - }, { - "val" : "FMA:15574" - }, { - "val" : "SCTID:29704000" + "val" : "RO:0002427" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009035", - "lbl" : "renal straight tubule", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "kidney straight tubule", - "xrefs" : [ "MA:0002634" ] - }, { - "pred" : "hasExactSynonym", - "val" : "straight tubule" - } ], - "xrefs" : [ { - "val" : "EMAPA:37489" - }, { - "val" : "MA:0002634" - }, { - "val" : "SCTID:245151008" - }, { - "val" : "Wikipedia:Tubuli_seminiferi_recti" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", - "lbl" : "entire embryonic mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Sum total of mesenchyme in the embryo.", - "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "xrefs" : [ { - "val" : "EHDAA2:0001113" - }, { - "val" : "EHDAA:177" - }, { - "val" : "EMAPA:16097" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009196", - "lbl" : "indifferent external genitalia", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], - "xrefs" : [ { - "val" : "EHDAA2:0004021" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009201", - "lbl" : "nephric duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A nephric duct is a tube that drains a primitive kidney[GO].", - "xrefs" : [ "GO:0072176" ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "pronephric duct or mesonephric duct" ], - "xrefs" : [ { - "val" : "EMAPA:16577" - }, { - "val" : "Wikipedia:Wolffian_duct" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", - "lbl" : "subdivision of trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "region of trunk", - "xrefs" : [ "FMA:25054" ] - }, { - "pred" : "hasExactSynonym", - "val" : "trunk subdivision", - "xrefs" : [ "FMA:25054" ] - } ], - "xrefs" : [ { - "val" : "FMA:25054" - }, { - "val" : "SCTID:22943007" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "exists during" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "lbl" : "trunk paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trunk and cervical paraxial mesenchyme", - "xrefs" : [ "EHDAA2:0002094" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trunk paraxial mesenchyme", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002094" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009773", - "lbl" : "renal tubule", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.", - "xrefs" : [ "DOI:10.1371/journal.pone.0099864", "GO:0061333", "GOC:dph", "GOC:mtg_kidney_jan10" ] + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "renal tubule (generic)", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "tubule of excretory system", - "xrefs" : [ "OBOL:automatic", "https://orcid.org/0000-0002-6601-2165" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009856", - "lbl" : "sac", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - 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In vertebrates, this is based on the vertebral column.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "axial subdivision of organism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "body segment" - }, { - "pred" : "hasRelatedSynonym", - "val" : "main body segment" + "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-1373-1705" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:26:52Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", - "lbl" : "embryonic cardiovascular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A cardiovascular system that is part of a conceptus.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "conceptus cardiovascular system" + "val" : "has sensory dendrite location" }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic circulatory system" + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" }, { - "pred" : "hasRelatedSynonym", - "val" : "fetal circulatory system" + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" } ], - "xrefs" : [ { - "val" : "EHDAA2:0000216" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-1373-1705" }, { - "val" : "FMA:305965" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1617-8244" }, { - "val" : "NCIT:C34148" - } ], + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1940-6740" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "lbl" : "coelom", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", - "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." }, "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "enterocoelom", - "xrefs" : [ "NCBITaxon:33511" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "haemocoelom" - }, { - "pred" : "hasNarrowSynonym", - "val" : "schizocoelom" + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { - "pred" : "hasRelatedSynonym", - "val" : "coelem" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { - "pred" : "hasRelatedSynonym", - "val" : "coelomic cavity", - "xrefs" : [ "EHDAA2:0004731" ] - } ], + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "lbl" : "results in changes to anatomical or cellular structure", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity" + }, "xrefs" : [ { - "val" : "EHDAA2:0004731" - }, { - "val" : "Wikipedia:Coelom" + "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_changes_to_anatomical_or_cellular_structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012274", - "lbl" : "columnar epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", + "lbl" : "obsolete has_high_plasma_membrane_amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].", - "xrefs" : [ "Wikipedia:Columnar_epithelium" ] + "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", + "xrefs" : [ "PMID:19243617" ] }, - "xrefs" : [ { - "val" : "Wikipedia:Columnar_epithelium" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0015015" + } ], + "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", - "lbl" : "meso-epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", + "lbl" : "obsolete has_low_plasma_membrane_amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", + "xrefs" : [ "PMID:19243617" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesoderm-derived epithelium" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" }, { - "pred" : "hasExactSynonym", - "val" : "mesoepithelium" - } ], - "xrefs" : [ { - "val" : "FMA:86452" + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0015016" } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", + "lbl" : "anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012292", - "lbl" : "embryonic cloacal fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "lbl" : "channel for", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly.", - "xrefs" : [ "MP:0011836", "MP:anna" ] - }, - "comments" : [ "We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts" ], "synonyms" : [ { "pred" : "hasBroadSynonym", - "val" : "cloacal fold", - "xrefs" : [ "EHDAA2:0004009" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0004009" + "val" : "carries" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -32884,303 +32139,164 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012361", - "lbl" : "internal anal region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", + "lbl" : "channels_from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "EHDAA2:0004588" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012469", - "lbl" : "external anal region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", + "lbl" : "channels_into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "EHDAA2:0004589" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012476", - "lbl" : "skeleton of pelvic complex", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "lbl" : "distally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "bones of lower limb", - "xrefs" : [ "FMA:24140" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "lower limb skeleton", - "xrefs" : [ "FMA:24140" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ossa membri inferioris", - "xrefs" : [ "FMA:TA" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pelvic complex skeleton", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of bones of lower limb", - "xrefs" : [ "FMA:24140" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "skeleton of posterior limb/fin and girdle", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } ], - "xrefs" : [ { - "val" : "FMA:24140" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013241", - "lbl" : "embryonic urethral groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", + "lbl" : "extends_fibers_into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The precursor of the urethra.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "sulcus urethralis primarius", - "xrefs" : [ "Wikipedia:Urethral_groove" ] - }, { - "pred" : "hasExactSynonym", - "val" : "urethral groove" - }, { - "pred" : "hasExactSynonym", - "val" : "urethral sulcus" - } ], - "xrefs" : [ { - "val" : "SCTID:361531004" - }, { - "val" : "Wikipedia:Urethral_groove" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", - "lbl" : "subdivision of tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", + "lbl" : "filtered through", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." + }, + "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013686", - "lbl" : "anatomical conduit space", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", + "lbl" : "indirectly_supplies", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].", - "xrefs" : [ "FMA:9338", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "foramen space" - } ], - "xrefs" : [ { - "val" : "FMA:9338" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "add to RO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "lbl" : "main body axis", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", + "lbl" : "layer part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", - "lbl" : "body proper", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", + "lbl" : "posteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The region of the organism associated with the visceral organs.", - "xrefs" : [ "AEO:0000103" ] + "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "body", - "xrefs" : [ "AEO:0000103" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "whole body", - "xrefs" : [ "BTO:0001489" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000103" - }, { - "val" : "BTO:0001489" - }, { - "val" : "FMA:231424" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013756", - "lbl" : "venous blood", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", + "lbl" : "protects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A blood that is part of a vein.", - "xrefs" : [ "OBOL:automatic" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blood in vein", - "xrefs" : [ "FMA:83067" ] - }, { - "pred" : "hasExactSynonym", - "val" : "portion of venous blood", - "xrefs" : [ "FMA:83067" ] - }, { - "pred" : "hasExactSynonym", - "val" : "venous blood", - "xrefs" : [ "FMA:83067" ] - } ], - "xrefs" : [ { - "val" : "FMA:83067" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013768", - "lbl" : "great vessel of heart", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", + "lbl" : "proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.", - "xrefs" : [ "Wikipedia:Great_vessels" ] + "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "comments" : [ "Groupings may vary - typically pulmonary vessels and aorta and vena cavae" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "great vessel" - }, { - "pred" : "hasExactSynonym", - "val" : "great vessel of thorax" - } ], - "xrefs" : [ { - "val" : "EMAPA:36460" - }, { - "val" : "SCTID:304066000" - }, { - "val" : "Wikipedia:Great_vessels" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", - "lbl" : "thoracic skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", + "lbl" : "sexually_homologous_to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", - "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "skeleton of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic part of axial skeleton" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic skeleton", - "xrefs" : [ "EHDAA2:0002013" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002013" - }, { - "val" : "FMA:77169" - }, { - "val" : "Wikipedia:Thoracic_skeleton" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", - "lbl" : "primordial vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", + "lbl" : "site_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A portion of tissue that will develop into vasculature.", - "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] + "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." }, - "xrefs" : [ { - "val" : "EFO:0003708" - }, { - "val" : "TAO:0005076" - }, { - "val" : "ZFA:0005076" + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "capable_of_has_part" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -33188,537 +32304,496 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "lbl" : "lateral structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", + "lbl" : "subdivision of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", - "lbl" : "circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "heart" - }, { - "pred" : "hasExactSynonym", - "val" : "cardiac pump" - }, { - "pred" : "hasExactSynonym", - "val" : "heart or heart like organ" - }, { - "pred" : "hasNarrowSynonym", - "val" : "circulatory vessel" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac structure" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", - "lbl" : "heart plus pericardium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", + "lbl" : "transitively distally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart/pericardium", - "xrefs" : [ "MA:0002449" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37597" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "val" : "MA:0002449" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", + "lbl" : "transitively proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", + "lbl" : "trunk_part_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016566", - "lbl" : "pit", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "An roughly circular indentation in a surface.", - "xrefs" : [ "AEO:0000204", "AEO:JB" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "AEO:0000204" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", - "lbl" : "future central nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "Primordium that develops into the central nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future CNS" - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive central nervous system" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", - "lbl" : "future nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Primordium that develops into the nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive nervous system", - "xrefs" : [ "AAO:0000477" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000477" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016887", - "lbl" : "entire extraembryonic component", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", - "xrefs" : [ "AEO:0000195", "AEO:JB" ] + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "extra-embryonic component" - }, { - "pred" : "hasExactSynonym", - "val" : "extraembryonic component", - "xrefs" : [ "AEO:0000195" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000195" - }, { - "val" : "EHDAA2:0000003" - }, { - "val" : "EMAPA:16042" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0018707", - "lbl" : "bladder organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A membranous sac in animals that serves as the receptacle of a liquid or contains gas.", - "xrefs" : [ "BTO:0000123" ] - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "bladder", - "xrefs" : [ "BTO:0000123" ] - } ], - "xrefs" : [ { - "val" : "BTO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], - "xrefs" : [ { - "val" : "CARO:0020001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034969", - "lbl" : "epithelial layer of duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "duct epithelium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ductal epithelium" - } ], - "xrefs" : [ { - "val" : "NCIT:C25787" - }, { - "val" : "UMLS:C1512086" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034996", - "lbl" : "outer renal medulla loop of Henle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "loop of Henle, outer medullary portion", - "xrefs" : [ "EMAPA:28322" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:28322" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034997", - "lbl" : "renal medulla loop of Henle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "loop of Henle of renal medulla", - "xrefs" : [ "EMAPA:35460" ] - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle, medullary portion" - } ], + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "xrefs" : [ { - "val" : "EMAPA:35460" + "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035554", - "lbl" : "right cardiac chamber", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Any chamber of the right side of the heart.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "xrefs" : [ { - "val" : "FMA:7165" - }, { - "val" : "SCTID:362007002" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], "xrefs" : [ { - "val" : "FMA:293105" + "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036146", - "lbl" : "cardiopharyngeal field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.", - "xrefs" : [ "http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1", "https://orcid.org/0000-0003-3308-6245" ] + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036215", - "lbl" : "anatomical surface region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity that forms the outermost boundary of an anatomical structure.", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/1324" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "AAO:0010270" - }, { - "val" : "ZFA:0005594" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036295", - "lbl" : "renal pelvis/ureter", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra.", - "xrefs" : [ "NCIT:C54419" ] + "val" : "A synonym type for describing abbreviations or initalisms" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "renal pelvis and ureter" - }, { - "pred" : "hasExactSynonym", - "val" : "renal pelvis plus ureter" - } ], - "xrefs" : [ { - "val" : "NCIT:C54419" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8410081", - "lbl" : "blood microvessel", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.", - "xrefs" : [ "Wikipedia:Microcirculation", "http://orcid.org/0000-0002-7073-9172" ] + "val" : "A synonym type for describing pluralization synonyms" }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "microvasculature" - }, { - "pred" : "hasBroadSynonym", - "val" : "microvessel" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-2825-0621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2186" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8450002", - "lbl" : "excretory system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An anatomical system that eliminates waste products that arise as a result of metabolic activity.", - "xrefs" : [ "GO:0007588" ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-6095-8718" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-05-25T18:21:29Z" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", - "lbl" : "visceral muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, - "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral muscle" - } ], + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:17:46Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { @@ -33730,6 +32805,7 @@ "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } @@ -33737,49 +32813,15 @@ "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { @@ -33787,291 +32829,391 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", "lbl" : "latin term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", "lbl" : "plural term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "type" : "PROPERTY", - "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." - }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "type" : "PROPERTY", - "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -34087,11 +33229,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -34108,6 +33252,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -34123,11 +33268,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -34143,23 +33290,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -34169,6 +33345,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -34352,14 +33540,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000134" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000064", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000064", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/GO_0005929" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -34368,14 +33548,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000483" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000067", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000064" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000067", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000066" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000068", "pred" : "is_a", @@ -34384,16 +33556,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000068", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000058" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000076", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "is_a", @@ -34442,8 +33604,8 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000213" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000133", "pred" : "is_a", @@ -34584,14 +33746,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000232", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000558" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000239", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000067" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000239", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000075" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", "pred" : "is_a", @@ -35061,7 +34215,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000666", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + "obj" : "http://purl.obolibrary.org/obo/CL_0000115" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000666", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002064" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000669", "pred" : "is_a", @@ -35349,21 +34507,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000115", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000666" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000666" + "obj" : "http://purl.obolibrary.org/obo/CL_0002681" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_1000746" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000074" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "is_a", @@ -35394,10 +34546,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002305", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004135" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002306", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000239" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002306", "pred" : "is_a", @@ -35725,13 +34873,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000612", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002584", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0002584" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000612", "pred" : "is_a", @@ -35787,13 +34929,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000746", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_1000612", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_1000612" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000746", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35830,10 +34966,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_1000849", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001292" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_1000854", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002584" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000854", "pred" : "is_a", @@ -35976,18 +35108,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_4033054", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002049" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000226", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007010" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000226", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007017" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000226", - "pred" : "http://purl.obolibrary.org/obo/RO_0002592", - "obj" : "http://purl.obolibrary.org/obo/GO_0015630" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000278", "pred" : "is_a", @@ -36024,18 +35144,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0001508", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0042391" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0001578", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0000226" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0001578", - "pred" : "http://purl.obolibrary.org/obo/RO_0000057", - "obj" : "http://purl.obolibrary.org/obo/GO_0005874" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0001578", - "pred" : "http://purl.obolibrary.org/obo/RO_0002297", - "obj" : "http://purl.obolibrary.org/obo/GO_0097427" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0001677", "pred" : "is_a", @@ -36370,34 +35478,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0005737", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005773", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043231" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005773", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - 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}, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1903047", "pred" : "is_a", @@ -38510,18 +37094,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_1903561", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0065010" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1905349", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0022607" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1905349", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0060271" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1905349", - "pred" : "http://purl.obolibrary.org/obo/RO_0002588", - "obj" : "http://purl.obolibrary.org/obo/GO_0035869" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1990904", "pred" : "is_a", @@ -38786,6 +37358,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002045", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000402" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002064", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002078", "pred" : "is_a", @@ -38802,10 +37378,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002198", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002226", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002266", "pred" : "is_a", @@ -38818,10 +37390,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002299", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002078" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002309", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002226" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002318", "pred" : "is_a", @@ -38866,6 +37434,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070047", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0070045" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -38998,6 +37578,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000050025", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000025", "pred" : "is_a", @@ -46302,6 +44886,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -46376,20 +44964,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0030219" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000064", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000067", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000068", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], @@ -46399,10 +44973,10 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000071", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000076" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0004638" + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", @@ -46679,6 +45253,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0002001" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000666", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002064" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000680", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0011115" ], @@ -47159,13 +45740,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002220", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000226", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0015630" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000278", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007049" ], @@ -47292,20 +45866,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007010", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005856" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007017", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007275", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], @@ -47379,13 +45939,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000479" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010970", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002341", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012501", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008219" ], @@ -47414,13 +45967,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016192", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0017145", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051301" ], @@ -47533,27 +46079,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002315", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000556" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030705", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0046907" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002341", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0099513" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031410", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031503", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032060", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -47561,13 +46086,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032059" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032838", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0120025" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032984", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022411" ], @@ -47575,13 +46093,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033365", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034101", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048872" ], @@ -47589,13 +46100,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0012003", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000232" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035082", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005930" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035148", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], @@ -47624,26 +46128,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035735", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0042073" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0060271" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042073", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002341", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043073", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005634" ], @@ -47707,20 +46191,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0003008" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0044782", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046907", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048103", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051301" ], @@ -47728,23 +46198,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000723" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048193", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002344", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005798" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048199", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006903" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002344", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005794" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005798" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048285", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], @@ -47829,41 +46282,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005694" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051640", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051648", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051649", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051650", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051656", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0055085", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -47871,13 +46289,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002342", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060271", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060429", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], @@ -47892,13 +46303,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002298", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003914" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061512", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0065003", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -47955,20 +46359,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002297", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003914" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097014", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097708", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098590", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -48014,33 +46404,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0015006" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099111", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099512", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0099080" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002309" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0015006" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099513", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0099512" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005856" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0015006" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099536", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007267" ], @@ -48048,13 +46411,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", "fillerId" : "http://purl.obolibrary.org/obo/GO_0045202" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099568", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0120025", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0042995" ], @@ -48107,13 +46463,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905349", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0035869" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PR_000029032", "genusIds" : [ "http://purl.obolibrary.org/obo/PR_000000001" ], @@ -49186,14 +47535,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0005634", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005794", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005929", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006915", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -49210,18 +47551,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0030097", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0042073", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0043009", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044782", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045202", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -49230,22 +47563,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050877", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0051640", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0051649", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0060271", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0061512", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0062023", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -49340,6 +47657,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/src/ontology/subsets/kidney_upper_slim.obo b/src/ontology/subsets/kidney_upper_slim.obo index 6bb9cf873..3f10ccd90 100644 --- a/src/ontology/subsets/kidney_upper_slim.obo +++ b/src/ontology/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -119,7 +124,7 @@ relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] @@ -133,7 +138,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -158,7 +163,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -206,7 +211,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -218,7 +223,7 @@ def: "A cell that is within the developmental lineage of gametes and is able to comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim subset: ubprop:upper_level -xref: ZFA:0009016 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: capable_of GO:0022414 ! reproductive process @@ -231,7 +236,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -254,7 +259,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -273,7 +278,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -291,7 +296,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -311,10 +316,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -330,24 +335,11 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000064 -name: ciliated cell -def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm] -subset: cellxgene_subset -xref: VHOG:0001532 -xref: XAO:0000031 -xref: ZFA:0009032 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell -intersection_of: CL:0000000 ! cell -intersection_of: has_part GO:0005929 ! cilium -relationship: has_part GO:0005929 ! cilium - [Term] id: CL:0000066 name: epithelial cell @@ -359,33 +351,21 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000067 -name: ciliated epithelial cell -def: "An epithelial cell that has a cilia." [GOC:tfm] -subset: cellxgene_subset -xref: FMA:70605 -xref: ZFA:0009035 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000064 ! ciliated cell -is_a: CL:0000066 ! epithelial cell -intersection_of: CL:0000066 ! epithelial cell -intersection_of: has_part GO:0005929 ! cilium - [Term] id: CL:0000068 name: duct epithelial cell def: "An epithelial cell that is part of a duct." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset -xref: ZFA:0009372 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009372 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000058 ! duct @@ -397,12 +377,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -419,7 +397,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -428,7 +406,7 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] @@ -439,7 +417,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -456,9 +434,9 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -466,7 +444,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -490,7 +468,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -533,14 +511,14 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -556,7 +534,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -566,7 +544,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -574,21 +552,21 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -600,7 +578,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -612,7 +590,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -622,7 +600,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -653,13 +631,6 @@ relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin r relationship: RO:0002202 CL:0000558 ! develops from reticulocyte property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000239 -name: brush border epithelial cell -xref: ZFA:0009143 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000067 ! ciliated epithelial cell -is_a: CL:0000075 ! columnar/cuboidal epithelial cell - [Term] id: CL:0000255 name: eukaryotic cell @@ -675,7 +646,7 @@ relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -686,7 +657,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -696,7 +667,7 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -724,14 +695,14 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -742,7 +713,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -759,16 +730,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -825,7 +796,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -846,7 +817,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -959,7 +930,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -997,7 +968,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1028,7 +999,7 @@ def: "A cell whose primary function is to support other cell types." [FB:ma, GOC subset: cellxgene_subset synonym: "supportive cell" EXACT [] xref: BTO:0002315 -xref: ZFA:0009387 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009387 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1040,7 +1011,7 @@ synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] xref: FMA:84138 -xref: ZFA:0005238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000192 ! smooth muscle cell is_a: CL:1000618 ! juxtaglomerular complex cell @@ -1061,17 +1032,21 @@ xref: BTO:0000853 xref: CALOHA:TS-0617 xref: FMA:70972 xref: MESH:D050527 -xref: ZFA:0009283 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009283 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000669 ! pericyte relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000666 -name: fenestrated cell +name: fenestrated endothelial cell +def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset synonym: "window cell" EXACT [] -xref: ZFA:0009286 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000066 ! epithelial cell +xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000115 ! endothelial cell +intersection_of: CL:0000115 ! endothelial cell +intersection_of: bearer_of PATO:0002064 ! fenestrated +relationship: bearer_of PATO:0002064 ! fenestrated [Term] id: CL:0000669 @@ -1088,7 +1063,7 @@ synonym: "pericyte cell" EXACT [] synonym: "pericyte of Rouget" EXACT [] xref: BTO:0002441 xref: FMA:63174 -xref: ZFA:0009112 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009112 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell @@ -1100,7 +1075,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1113,7 +1088,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1127,7 +1102,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1144,7 +1119,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -1159,7 +1134,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -1205,7 +1180,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -1253,7 +1228,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1273,7 +1248,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1287,7 +1262,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1301,7 +1276,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1309,12 +1284,12 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1323,12 +1298,12 @@ name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1343,7 +1318,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1361,7 +1336,7 @@ is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium relationship: part_of UBERON:0002321 ! extraglomerular mesangium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:20:55Z [Term] @@ -1372,12 +1347,12 @@ subset: cellxgene_subset subset: kidney_upper_slim xref: BTO:0004632 xref: FMA:70970 -is_a: CL:0000115 {is_inferred="true"} ! endothelial cell -is_a: CL:0000666 ! fenestrated cell -is_a: CL:1000746 ! glomerular cell +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +relationship: part_of UBERON:0000074 ! renal glomerulus +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z [Term] @@ -1389,7 +1364,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1411,13 +1386,13 @@ relationship: part_of UBERON:0004135 ! distal tubule id: CL:0002306 name: epithelial cell of proximal tubule def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1-4160-2328-3] +comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. subset: cellxgene_subset subset: human_reference_atlas subset: kidney_upper_slim synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:70973 xref: KUPO:0001044 -is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell @@ -1437,7 +1412,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1448,12 +1423,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1463,9 +1438,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1482,7 +1457,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1491,12 +1466,12 @@ name: kidney epithelial cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] subset: cellxgene_subset xref: KUPO:0001019 -xref: ZFA:0009374 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009374 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 {is_inferred="true"} ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z [Term] @@ -1504,9 +1479,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1527,7 +1502,7 @@ is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001225 ! cortex of kidney -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0956-8634 +property_value: terms:contributor https://orcid.org/0000-0002-0956-8634 creation_date: 2011-10-25T03:49:41Z [Term] @@ -1535,7 +1510,7 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset -xref: ZFA:0005322 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell @@ -1543,11 +1518,11 @@ is_a: CL:0002518 ! kidney epithelial cell id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -1567,7 +1542,7 @@ is_a: CL:0000988 ! hematopoietic cell id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -1592,10 +1567,10 @@ def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0005944 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005944 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033054 ! perivascular cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T17:33:55Z [Term] @@ -1623,7 +1598,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -1645,7 +1620,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -1656,7 +1631,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -1667,7 +1642,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -1734,7 +1709,7 @@ name: kidney cell def: "A cell that is part of a kidney." [] subset: cellxgene_subset xref: KUPO:0001010 -xref: ZFA:0009389 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002113 ! kidney @@ -1747,7 +1722,7 @@ def: "A cell that is part of kidney interstitium." [] subset: cellxgene_subset subset: kidney_upper_slim xref: KUPO:0001013 -xref: ZFA:0009390 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009390 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell is_a: CL:4030031 ! interstitial cell intersection_of: CL:1000497 ! kidney cell @@ -1759,7 +1734,7 @@ id: CL:1000504 name: kidney medulla cell def: "A cell that is part of a renal medulla." [PMID:22343825] xref: KUPO:0001017 -xref: ZFA:0009391 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009391 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0000362 ! renal medulla @@ -1827,7 +1802,7 @@ name: kidney corpuscule cell def: "Any renal cortical epithelial cell that is part of some renal corpuscle." [FBC:Autogenerated] subset: kidney_upper_slim xref: KUPO:0001021 -is_a: CL:0002584 {is_inferred="true"} ! renal cortical epithelial cell +is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron intersection_of: CL:0002584 ! renal cortical epithelial cell intersection_of: part_of UBERON:0001229 ! renal corpuscle @@ -1876,7 +1851,7 @@ id: CL:1000746 name: glomerular cell def: "Any kidney corpuscule cell that is part of some renal glomerulus." [FBC:Autogenerated] xref: KUPO:0001036 -is_a: CL:1000612 {is_inferred="true"} ! kidney corpuscule cell +is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus @@ -1915,7 +1890,6 @@ id: CL:1000854 name: kidney blood vessel cell def: "A blood vessel cell that is part of a kidney." [PMID:34843404] xref: KUPO:0001014 -is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel @@ -2025,7 +1999,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue -property_value: http://purl.org/dc/terms/date "2022-11-30T14:35:08Z" xsd:dateTime +property_value: terms:date "2022-11-30T14:35:08Z" xsd:dateTime [Term] id: CL:4033054 @@ -2035,31 +2009,15 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature relationship: adjacent_to UBERON:0002049 ! vasculature -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-22T13:40:28Z" xsd:dateTime - -[Term] -id: GO:0000226 -name: microtubule cytoskeleton organization -namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] -subset: goslim_pombe -synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah] -synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah] -is_a: GO:0007010 ! cytoskeleton organization -is_a: GO:0007017 ! microtubule-based process -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0015630 ! microtubule cytoskeleton -relationship: results_in_organization_of GO:0015630 ! microtubule cytoskeleton -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23114" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23195" xsd:anyURI +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -2126,16 +2084,6 @@ comment: Action potentials typically propagate across excitable membranes. This is_a: GO:0042391 ! regulation of membrane potential property_value: RO:0002161 NCBITaxon:4895 -[Term] -id: GO:0001578 -name: microtubule bundle formation -namespace: biological_process -def: "A process that results in a parallel arrangement of microtubules." [GOC:dph] -synonym: "microtubule bundling" EXACT [] -is_a: GO:0000226 ! microtubule cytoskeleton organization -relationship: has_participant GO:0005874 ! microtubule -relationship: results_in_formation_of GO:0097427 ! microtubule bundle - [Term] id: GO:0001677 name: formation of translation initiation ternary complex @@ -2657,67 +2605,6 @@ is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI -[Term] -id: GO:0005773 -name: vacuole -namespace: cellular_component -def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_yeast -synonym: "vacuolar carboxypeptidase Y" RELATED [] -xref: Wikipedia:Vacuole -is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: part_of GO:0005737 ! cytoplasm - -[Term] -id: GO:0005794 -name: Golgi apparatus -namespace: cellular_component -def: "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways." [ISBN:0198506732] -comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_generic -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_yeast -synonym: "Golgi" BROAD [] -synonym: "Golgi complex" EXACT [] -synonym: "Golgi ribbon" NARROW [] -xref: NIF_Subcellular:sao451912436 -xref: Wikipedia:Golgi_apparatus -is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0012505 ! endomembrane system -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota - -[Term] -id: GO:0005798 -name: Golgi-associated vesicle -namespace: cellular_component -def: "Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell." [GOC:mah] -comment: Note that this definition includes vesicles that are transiently associated with the Golgi. -synonym: "Golgi vesicle" RELATED [] -synonym: "vesicular component" RELATED [NIF_Subcellular:sao138219748] -xref: NIF_Subcellular:sao819927218 -is_a: GO:0031410 ! cytoplasmic vesicle - [Term] id: GO:0005840 name: ribosome @@ -2744,41 +2631,6 @@ is_a: GO:0043232 ! intracellular non-membrane-bounded organelle relationship: capable_of_part_of GO:0006412 ! translation relationship: has_part PR:000000001 ! protein -[Term] -id: GO:0005856 -name: cytoskeleton -namespace: cellular_component -def: "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, PMID:16959967, PMID:27419875] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_prokaryote -subset: goslim_yeast -xref: Wikipedia:Cytoskeleton -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle - -[Term] -id: GO:0005874 -name: microtubule -namespace: cellular_component -def: "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." [ISBN:0879693568] -subset: goslim_metagenomics -synonym: "microtubuli" EXACT [] -synonym: "microtubulus" EXACT [] -synonym: "neurotubule" NARROW [NIF_Subcellular:sao248349196] -xref: NIF_Subcellular:sao1846835077 -xref: Wikipedia:Microtubule -is_a: GO:0099513 ! polymeric cytoskeletal fiber -relationship: part_of GO:0015630 ! microtubule cytoskeleton - [Term] id: GO:0005886 name: plasma membrane @@ -2826,55 +2678,6 @@ xref: NIF_Subcellular:sao1922892319 is_a: GO:0070161 ! anchoring junction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22122" xsd:anyURI -[Term] -id: GO:0005929 -name: cilium -namespace: cellular_component -alt_id: GO:0072372 -def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_pir -synonym: "eukaryotic flagellum" EXACT [] -synonym: "flagellum" RELATED [] -synonym: "microtubule-based flagellum" EXACT [] -synonym: "primary cilium" NARROW [] -xref: FMA:67181 -xref: NIF_Subcellular:sao787716553 -xref: Wikipedia:Cilium -is_a: GO:0043227 ! membrane-bounded organelle -is_a: GO:0120025 ! plasma membrane bounded cell projection -relationship: has_part GO:0030990 ! intraciliary transport particle -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 - -[Term] -id: GO:0005930 -name: axoneme -namespace: cellular_component -alt_id: GO:0035085 -alt_id: GO:0035086 -def: "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, ISBN:0198547684] -comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. -subset: goslim_pir -synonym: "ciliary axoneme" EXACT [] -synonym: "cilium axoneme" EXACT [] -synonym: "flagellar axoneme" EXACT [] -synonym: "flagellum axoneme" EXACT [] -xref: Wikipedia:Axoneme -is_a: GO:0110165 ! cellular anatomical entity -relationship: has_part GO:0005874 ! microtubule -relationship: part_of GO:0005856 ! cytoskeleton -relationship: part_of GO:0097014 ! ciliary plasm - [Term] id: GO:0006412 name: translation @@ -2990,15 +2793,6 @@ namespace: biological_process def: "The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] is_a: GO:0042044 ! fluid transport -[Term] -id: GO:0006903 -name: vesicle targeting -namespace: biological_process -def: "The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo." [GOC:mah, PMID:17335816] -is_a: GO:0009987 ! cellular process -relationship: part_of GO:0016192 ! vesicle-mediated transport -relationship: part_of GO:0051650 ! establishment of vesicle localization - [Term] id: GO:0006915 name: apoptotic process @@ -3076,47 +2870,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-19T15:25:51Z -[Term] -id: GO:0007010 -name: cytoskeleton organization -namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_prokaryote -subset: goslim_yeast -synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah] -synonym: "cytoskeletal regulator activity" RELATED [] -synonym: "cytoskeleton organisation" EXACT [] -synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah] -is_a: GO:0006996 ! organelle organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0005856 ! cytoskeleton -relationship: results_in_organization_of GO:0005856 ! cytoskeleton - -[Term] -id: GO:0007017 -name: microtubule-based process -namespace: biological_process -def: "Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins." [GOC:mah] -subset: goslim_chembl -is_a: GO:0009987 ! cellular process -intersection_of: GO:0009987 ! cellular process -intersection_of: process_has_causal_agent GO:0005874 ! microtubule -relationship: process_has_causal_agent GO:0005874 ! microtubule -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI - -[Term] -id: GO:0007018 -name: microtubule-based movement -namespace: biological_process -def: "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194] -subset: goslim_drosophila -subset: goslim_generic -is_a: GO:0007017 ! microtubule-based process - [Term] id: GO:0007049 name: cell cycle @@ -3454,7 +3207,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3591,23 +3343,6 @@ is_a: GO:0009059 ! macromolecule biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22557" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25419" xsd:anyURI -[Term] -id: GO:0010970 -name: transport along microtubule -namespace: biological_process -def: "The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity." [GOC:dph, GOC:mah, GOC:tb] -synonym: "establishment of localization by movement along microtubule" EXACT [GOC:dph] -synonym: "microtubule-based transport" BROAD [] -synonym: "movement along microtubule" EXACT [] -is_a: GO:0007018 ! microtubule-based movement -is_a: GO:0030705 ! cytoskeleton-dependent intracellular transport -is_a: GO:0099111 ! microtubule-based transport -intersection_of: GO:0006810 ! transport -intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: results_in_transport_along GO:0005874 ! microtubule -created_by: tb -creation_date: 2009-05-27T10:56:08Z - [Term] id: GO:0012501 name: programmed cell death @@ -3638,20 +3373,6 @@ intersection_of: starts_with GO:0007165 ! signal transduction relationship: starts_with GO:0007165 ! signal transduction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24835" xsd:anyURI -[Term] -id: GO:0012505 -name: endomembrane system -namespace: cellular_component -def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh] -subset: goslim_candida -subset: goslim_flybase_ribbon -subset: goslim_yeast -xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity -relationship: has_part GO:0005773 ! vacuole -relationship: has_part GO:0005886 ! plasma membrane -relationship: part_of CL:0000000 ! cell - [Term] id: GO:0015031 name: protein transport @@ -3662,18 +3383,11 @@ subset: goslim_chembl subset: goslim_pir subset: goslim_yeast synonym: "enzyme transport" NARROW [] +is_a: GO:0006810 ! transport is_a: GO:0045184 ! establishment of protein localization -is_a: GO:0071702 ! organic substance transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input PR:000000001 ! protein -[Term] -id: GO:0015630 -name: microtubule cytoskeleton -namespace: cellular_component -def: "The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins." [GOC:jl, ISBN:0395825172] -is_a: GO:0005856 ! cytoskeleton - [Term] id: GO:0015669 name: gas transport @@ -3754,31 +3468,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0031982 ! vesicle relationship: results_in_organization_of GO:0031982 ! vesicle -[Term] -id: GO:0016192 -name: vesicle-mediated transport -namespace: biological_process -alt_id: GO:0006899 -def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_generic -subset: goslim_pir -subset: goslim_pombe -synonym: "nonselective vesicle transport" NARROW [] -synonym: "protein sorting along secretory pathway" RELATED [] -synonym: "vesicle trafficking" RELATED [] -synonym: "vesicle transport" EXACT [] -synonym: "vesicular transport" EXACT [GOC:mah] -is_a: GO:0006810 ! transport -is_a: GO:0009987 ! cellular process -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0031982 ! vesicle -relationship: process_has_causal_agent GO:0031982 ! vesicle -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25421" xsd:anyURI - [Term] id: GO:0016331 name: morphogenesis of embryonic epithelium @@ -3885,14 +3574,6 @@ intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0007049 ! cell cycle relationship: part_of GO:0007049 ! cell cycle -[Term] -id: GO:0022406 -name: membrane docking -namespace: biological_process -def: "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere." [GOC:isa_complete, PMID:27875684] -subset: goslim_pir -is_a: GO:0009987 ! cellular process - [Term] id: GO:0022411 name: cellular component disassembly @@ -4027,7 +3708,7 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -4042,7 +3723,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -4055,7 +3736,7 @@ relationship: results_in_assembly_of GO:0042995 ! cell projection id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -4182,31 +3863,6 @@ is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery -[Term] -id: GO:0030705 -name: cytoskeleton-dependent intracellular transport -namespace: biological_process -def: "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell." [GOC:mah] -subset: goslim_chembl -subset: goslim_drosophila -is_a: GO:0046907 ! intracellular transport -intersection_of: GO:0046907 ! intracellular transport -intersection_of: results_in_transport_along GO:0099513 ! polymeric cytoskeletal fiber -relationship: results_in_transport_along GO:0099513 ! polymeric cytoskeletal fiber - -[Term] -id: GO:0030990 -name: intraciliary transport particle -namespace: cellular_component -def: "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules." [GOC:cilia, GOC:kmv, PMID:14570576, PMID:22118932, PMID:23945166] -comment: Note that we deem cilia and microtubule-based flagella to be equivalent. -subset: goslim_pir -synonym: "IFT complex" RELATED [] -synonym: "intraflagellar transport complex" EXACT [] -synonym: "intraflagellar transport particle" EXACT [] -is_a: GO:0032991 ! protein-containing complex -relationship: capable_of_part_of GO:0035735 ! intraciliary transport involved in cilium assembly - [Term] id: GO:0031012 name: extracellular matrix @@ -4227,46 +3883,6 @@ is_a: GO:0030312 ! external encapsulating structure disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -[Term] -id: GO:0031410 -name: cytoplasmic vesicle -namespace: cellular_component -alt_id: GO:0016023 -def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_generic -subset: goslim_mouse -subset: goslim_yeast -synonym: "cytoplasmic membrane bounded vesicle" RELATED [] -synonym: "cytoplasmic membrane-enclosed vesicle" RELATED [] -synonym: "cytoplasmic, membrane-bounded vesicle" RELATED [] -xref: NIF_Subcellular:sao180601769 -is_a: GO:0097708 ! intracellular vesicle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - -[Term] -id: GO:0031503 -name: protein-containing complex localization -namespace: biological_process -alt_id: GO:0034629 -def: "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location." [GOC:mah] -synonym: "cellular protein complex localisation" RELATED [GOC:mah] -synonym: "cellular protein complex localization" RELATED [] -synonym: "cellular protein-containing complex localization" RELATED [] -synonym: "establishment and maintenance of cellular protein complex localization" RELATED [] -synonym: "establishment and maintenance of protein complex localization" EXACT [] -synonym: "protein complex localisation" EXACT [GOC:mah] -synonym: "protein complex localization" RELATED [] -is_a: GO:0051179 ! localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0032991 ! protein-containing complex -relationship: has_primary_input GO:0032991 ! protein-containing complex -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22021" xsd:anyURI - [Term] id: GO:0031974 name: membrane-enclosed lumen @@ -4357,16 +3973,6 @@ is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-19T12:21:31Z -[Term] -id: GO:0032838 -name: plasma membrane bounded cell projection cytoplasm -namespace: cellular_component -def: "All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection." [GOC:krc, GOC:mah] -is_a: GO:0099568 ! cytoplasmic region -intersection_of: GO:0005737 ! cytoplasm -intersection_of: part_of GO:0120025 ! plasma membrane bounded cell projection -relationship: part_of GO:0120025 ! plasma membrane bounded cell projection - [Term] id: GO:0032940 name: secretion by cell @@ -4437,18 +4043,6 @@ subset: goslim_flybase_ribbon synonym: "macromolecule localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization -[Term] -id: GO:0033365 -name: protein localization to organelle -namespace: biological_process -def: "A process in which a protein is transported to, or maintained in, a location within an organelle." [GOC:mah] -synonym: "protein localisation to organelle" EXACT [GOC:mah] -synonym: "protein localization in organelle" EXACT [GOC:mah] -is_a: GO:0008104 ! protein localization -intersection_of: GO:0008104 ! protein localization -intersection_of: has_target_end_location GO:0043226 ! organelle -relationship: has_target_end_location GO:0043226 ! organelle - [Term] id: GO:0034101 name: erythrocyte homeostasis @@ -4475,27 +4069,6 @@ synonym: "transmembrane ion transport" EXACT [GOC:dph, GOC:tb] is_a: GO:0006811 ! monoatomic ion transport is_a: GO:0055085 ! transmembrane transport -[Term] -id: GO:0035082 -name: axoneme assembly -namespace: biological_process -alt_id: GO:0035083 -alt_id: GO:0035084 -def: "The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, GOC:jl, ISBN:0815316194] -comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. -synonym: "axoneme biogenesis" RELATED [GOC:mah] -synonym: "ciliary axoneme assembly" EXACT [] -synonym: "cilium axoneme assembly" EXACT [] -synonym: "cilium axoneme biogenesis" RELATED [GOC:mah] -synonym: "flagellar axoneme assembly" EXACT [] -synonym: "flagellum axoneme assembly" EXACT [] -is_a: GO:0001578 ! microtubule bundle formation -is_a: GO:0022607 ! cellular component assembly -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0005930 ! axoneme -relationship: part_of GO:0060271 ! cilium assembly -relationship: results_in_assembly_of GO:0005930 ! axoneme - [Term] id: GO:0035148 name: tube formation @@ -4545,36 +4118,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region created_by: bf creation_date: 2010-11-09T10:25:08Z -[Term] -id: GO:0035735 -name: intraciliary transport involved in cilium assembly -namespace: biological_process -def: "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly." [GOC:bf, GOC:cilia, Reactome:R-HSA-5620924.2] -synonym: "intraciliary transport involved in cilium morphogenesis" RELATED [] -synonym: "intraflagellar transport" BROAD [] -synonym: "intraflagellar transport involved in cilium morphogenesis" RELATED [] -xref: Reactome:R-HSA-5620924.2 -is_a: GO:0042073 ! intraciliary transport -intersection_of: GO:0042073 ! intraciliary transport -intersection_of: part_of GO:0060271 ! cilium assembly -relationship: part_of GO:0060271 ! cilium assembly -created_by: bf -creation_date: 2011-03-17T10:55:42Z - -[Term] -id: GO:0035869 -name: ciliary transition zone -namespace: cellular_component -def: "A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm." [GOC:cilia, GOC:kmv, PMID:21422230] -comment: Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone. -synonym: "cilial transition zone" EXACT [] -synonym: "cilium transition zone" EXACT [] -synonym: "connecting cilium" RELATED [] -is_a: GO:0110165 ! cellular anatomical entity -relationship: part_of GO:0005929 ! cilium -created_by: bf -creation_date: 2011-05-25T03:09:58Z - [Term] id: GO:0040011 name: locomotion @@ -4601,35 +4144,6 @@ def: "The directed movement of substances that are in liquid form in normal livi subset: goslim_pir is_a: GO:0006810 ! transport -[Term] -id: GO:0042073 -name: intraciliary transport -namespace: biological_process -alt_id: GO:0035734 -def: "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374, Reactome:R-HSA-5620924.2] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. -synonym: "IFT" RELATED [] -synonym: "intraflagellar transport" EXACT [] -synonym: "intraflagellar transport involved in cilium organization" EXACT [] -synonym: "intraflagellar transport involved in microtubule-based flagellum organisation" EXACT [] -xref: Wikipedia:Intraflagellar_transport -is_a: GO:0010970 ! transport along microtubule -is_a: GO:0031503 ! protein-containing complex localization -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input GO:0032991 ! protein-containing complex -intersection_of: occurs_in GO:0005929 ! cilium -intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: occurs_in GO:0005929 ! cilium -relationship: part_of GO:0044782 ! cilium organization -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 - [Term] id: GO:0042391 name: regulation of membrane potential @@ -4660,7 +4174,7 @@ is_a: GO:0008150 ! biological_process id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -4881,13 +4395,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -4906,25 +4421,6 @@ is_a: GO:0009058 ! biosynthetic process is_a: GO:0044237 ! cellular metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -[Term] -id: GO:0044782 -name: cilium organization -namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:cilia, GOC:jl] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. -subset: goslim_drosophila -subset: goslim_generic -synonym: "microtubule-based flagellum organization" EXACT [] -is_a: GO:0006996 ! organelle organization -is_a: GO:0120036 ! plasma membrane bounded cell projection organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0005929 ! cilium -relationship: results_in_organization_of GO:0005929 ! cilium -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -created_by: jl -creation_date: 2013-03-27T15:09:58Z - [Term] id: GO:0045184 name: establishment of protein localization @@ -4965,23 +4461,6 @@ def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport -[Term] -id: GO:0046907 -name: intracellular transport -namespace: biological_process -alt_id: GO:1902582 -def: "The directed movement of substances within a cell." [GOC:ai] -synonym: "single organism intracellular transport" RELATED [GOC:TermGenie] -synonym: "single-organism intracellular transport" RELATED [] -is_a: GO:0006810 ! transport -is_a: GO:0051641 ! cellular localization -is_a: GO:0051649 ! establishment of localization in cell -intersection_of: GO:0006810 ! transport -intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure -relationship: occurs_in GO:0005622 ! intracellular anatomical structure -created_by: jl -creation_date: 2013-12-18T14:04:50Z - [Term] id: GO:0048103 name: somatic stem cell division @@ -4993,34 +4472,6 @@ intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000723 ! somatic stem cell relationship: has_primary_input CL:0000723 ! somatic stem cell -[Term] -id: GO:0048193 -name: Golgi vesicle transport -namespace: biological_process -def: "The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles." [GOC:jid, ISBN:0716731363, PMID:10219233] -subset: goslim_yeast -synonym: "Golgi-derived vesicle transport" RELATED [] -is_a: GO:0016192 ! vesicle-mediated transport -intersection_of: GO:0006810 ! transport -intersection_of: results_in_transport_to_from_or_in GO:0005798 ! Golgi-associated vesicle -relationship: results_in_transport_to_from_or_in GO:0005798 ! Golgi-associated vesicle - -[Term] -id: GO:0048199 -name: vesicle targeting, to, from or within Golgi -namespace: biological_process -def: "The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation." [GOC:jid, GOC:mah, ISBN:0716731363, PMID:10219233] -synonym: "dictyosome vesicle targeting" NARROW [] -synonym: "Golgi vesicle targeting" EXACT [] -synonym: "vesicle targeting, to, from or within dictyosome" NARROW [] -is_a: GO:0006903 ! vesicle targeting -intersection_of: GO:0006903 ! vesicle targeting -intersection_of: has_primary_input GO:0005798 ! Golgi-associated vesicle -intersection_of: results_in_transport_to_from_or_in GO:0005794 ! Golgi apparatus -relationship: has_primary_input GO:0005798 ! Golgi-associated vesicle -relationship: part_of GO:0048193 ! Golgi vesicle transport -relationship: results_in_transport_to_from_or_in GO:0005794 ! Golgi apparatus - [Term] id: GO:0048285 name: organelle fission @@ -5374,22 +4825,6 @@ subset: goslim_pir xref: Wikipedia:Cell_division is_a: GO:0009987 ! cellular process -[Term] -id: GO:0051640 -name: organelle localization -namespace: biological_process -def: "Any process in which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai] -subset: goslim_pir -synonym: "establishment and maintenance of organelle localization" EXACT [] -synonym: "organelle localisation" EXACT [GOC:mah] -is_a: GO:0051179 ! localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0043226 ! organelle -relationship: has_primary_input GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI - [Term] id: GO:0051641 name: cellular localization @@ -5412,60 +4847,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-18T14:04:32Z -[Term] -id: GO:0051648 -name: vesicle localization -namespace: biological_process -def: "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:ai] -synonym: "cytoplasmic vesicle localization" EXACT [] -synonym: "establishment and maintenance of vesicle localization" EXACT [] -synonym: "vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051640 ! organelle localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0031982 ! vesicle -relationship: has_primary_input GO:0031982 ! vesicle - -[Term] -id: GO:0051649 -name: establishment of localization in cell -namespace: biological_process -def: "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] -synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] -synonym: "establishment of intracellular localization" NARROW [] -synonym: "establishment of localisation in cell" EXACT [GOC:mah] -synonym: "establishment of localization within cell" NARROW [] -synonym: "positioning within cell" NARROW [] -is_a: GO:0051234 ! establishment of localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: occurs_in CL:0000000 ! cell -relationship: occurs_in CL:0000000 ! cell -relationship: part_of GO:0051641 ! cellular localization -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms -relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms - -[Term] -id: GO:0051650 -name: establishment of vesicle localization -namespace: biological_process -def: "The directed movement of a vesicle to a specific location." [GOC:ai] -synonym: "establishment of vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051648 ! vesicle localization -is_a: GO:0051649 ! establishment of localization in cell -is_a: GO:0051656 ! establishment of organelle localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: has_primary_input GO:0031982 ! vesicle - -[Term] -id: GO:0051656 -name: establishment of organelle localization -namespace: biological_process -def: "The directed movement of an organelle to a specific location." [GOC:ai] -synonym: "establishment of organelle localisation" EXACT [GOC:mah] -is_a: GO:0051234 ! establishment of localization -is_a: GO:0051640 ! organelle localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: has_primary_input GO:0043226 ! organelle - [Term] id: GO:0051716 name: cellular response to stimulus @@ -5510,40 +4891,6 @@ xref: Wikipedia:Urination is_a: GO:0003014 ! renal system process is_a: GO:0007588 ! excretion -[Term] -id: GO:0060271 -name: cilium assembly -namespace: biological_process -alt_id: GO:0042384 -def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. -synonym: "ciliogenesis" EXACT [] -synonym: "cilium biogenesis" RELATED [GOC:mah] -synonym: "cilium formation" EXACT [] -synonym: "cilium morphogenesis" RELATED [] -synonym: "cilium organization" RELATED [GOC:dph] -synonym: "microtubule-based flagellum assembly" EXACT [] -xref: Reactome:R-HSA-5617833.2 -is_a: GO:0044782 ! cilium organization -is_a: GO:0070925 ! organelle assembly -is_a: GO:0120031 ! plasma membrane bounded cell projection assembly -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0005929 ! cilium -relationship: has_part GO:0035082 ! axoneme assembly -relationship: has_part GO:0035735 ! intraciliary transport involved in cilium assembly -relationship: has_part GO:0061512 ! protein localization to cilium -relationship: has_part GO:0097712 ! vesicle targeting, trans-Golgi to periciliary membrane compartment -relationship: has_part GO:1905349 ! ciliary transition zone assembly -relationship: results_in_assembly_of GO:0005929 ! cilium -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -relationship: starts_with GO:0097711 ! ciliary basal body-plasma membrane docking -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 - [Term] id: GO:0060429 name: epithelium development @@ -5578,26 +4925,6 @@ is_a: GO:0002009 ! morphogenesis of an epithelium created_by: dph creation_date: 2010-05-25T09:05:34Z -[Term] -id: GO:0061512 -name: protein localization to cilium -namespace: biological_process -def: "A process in which a protein is transported to, or maintained in, a location within a cilium." [GOC:dph] -is_a: GO:0033365 ! protein localization to organelle -intersection_of: GO:0008104 ! protein localization -intersection_of: has_target_end_location GO:0005929 ! cilium -relationship: has_target_end_location GO:0005929 ! cilium -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 -created_by: dph -creation_date: 2013-03-22T15:41:44Z - [Term] id: GO:0062023 name: collagen-containing extracellular matrix @@ -5756,29 +5083,6 @@ relationship: has_target_end_location GO:0005576 ! extracellular region created_by: mah creation_date: 2010-02-25T04:00:13Z -[Term] -id: GO:0071702 -name: organic substance transport -namespace: biological_process -def: "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [GOC:mah] -is_a: GO:0006810 ! transport -created_by: mah -creation_date: 2010-03-08T02:15:14Z - -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071826 name: protein-RNA complex organization @@ -5853,27 +5157,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: mah creation_date: 2010-02-26T02:15:40Z -[Term] -id: GO:0097014 -name: ciliary plasm -namespace: cellular_component -def: "All of the contents of a cilium, excluding the plasma membrane surrounding the cilium." [GOC:BHF, GOC:cilia, GOC:dos, PMID:17895364] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". -synonym: "cilial cytoplasm" RELATED [] -synonym: "ciliary cytoplasm" RELATED [] -synonym: "cilium cytoplasm" RELATED [] -synonym: "cilium plasm" EXACT [] -synonym: "microtubule-based flagellar cytoplasm" RELATED [] -synonym: "microtubule-based flagellar matrix" NARROW [] -synonym: "microtubule-based flagellum cytoplasm" RELATED [] -synonym: "microtubule-based flagellum matrix" NARROW [] -is_a: GO:0032838 ! plasma membrane bounded cell projection cytoplasm -intersection_of: GO:0005737 ! cytoplasm -intersection_of: part_of GO:0005929 ! cilium -relationship: part_of GO:0005929 ! cilium -created_by: pr -creation_date: 2011-03-23T01:52:31Z - [Term] id: GO:0097190 name: apoptotic signaling pathway @@ -5921,55 +5204,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pr creation_date: 2012-03-05T02:03:58Z -[Term] -id: GO:0097427 -name: microtubule bundle -namespace: cellular_component -def: "An arrangement of closely apposed microtubules running parallel to each other." [NIF_Subcellular:sao1872343973] -synonym: "microtubule fascicle" EXACT [] -xref: NIF_Subcellular:sao1872343973 -is_a: GO:0110165 ! cellular anatomical entity -relationship: has_part GO:0005874 ! microtubule -relationship: part_of GO:0005856 ! cytoskeleton -created_by: pr -creation_date: 2012-11-07T15:01:27Z - -[Term] -id: GO:0097708 -name: intracellular vesicle -namespace: cellular_component -def: "Any vesicle that is part of the intracellular region." [GOC:vesicles] -is_a: GO:0031982 ! vesicle -is_a: GO:0043231 ! intracellular membrane-bounded organelle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr -creation_date: 2016-03-29T17:39:45Z - -[Term] -id: GO:0097711 -name: ciliary basal body-plasma membrane docking -namespace: biological_process -def: "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane." [GOC:cilia, PMID:13978319, PMID:23348840, PMID:23530209, PMID:25686250, PMID:26981235, Reactome:R-HSA-5620912.1] -comment: Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella. -synonym: "anchoring of the basal body to the plasma membrane" RELATED [] -synonym: "ciliary basal body docking" EXACT [] -xref: Reactome:R-HSA-5620912.1 -is_a: GO:0140056 ! organelle localization by membrane tethering -relationship: part_of GO:0060271 ! cilium assembly -created_by: pr -creation_date: 2016-08-05T16:12:33Z - -[Term] -id: GO:0097712 -name: vesicle targeting, trans-Golgi to periciliary membrane compartment -namespace: biological_process -def: "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces." [GOC:cilia, PMID:20106869, PMID:23351793, PMID:24814148, PMID:26485645, Reactome:R-HSA-5620920.1] -is_a: GO:0048199 ! vesicle targeting, to, from or within Golgi -relationship: part_of GO:0060271 ! cilium assembly -created_by: pr -creation_date: 2016-08-05T16:16:28Z - [Term] id: GO:0097734 name: extracellular exosome biogenesis @@ -6098,40 +5332,6 @@ intersection_of: GO:0099080 ! supramolecular complex intersection_of: bearer_of PATO:0015006 ! polymeric relationship: bearer_of PATO:0015006 ! polymeric -[Term] -id: GO:0099111 -name: microtubule-based transport -namespace: biological_process -def: "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194] -is_a: GO:0006810 ! transport -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0005874 ! microtubule -relationship: process_has_causal_agent GO:0005874 ! microtubule - -[Term] -id: GO:0099512 -name: supramolecular fiber -namespace: cellular_component -alt_id: GO:0043205 -def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] -synonym: "fibril" RELATED [] -is_a: GO:0099081 ! supramolecular polymer -intersection_of: GO:0099080 ! supramolecular complex -intersection_of: bearer_of PATO:0002309 ! fiber shaped -intersection_of: bearer_of PATO:0015006 ! polymeric -relationship: bearer_of PATO:0002309 ! fiber shaped - -[Term] -id: GO:0099513 -name: polymeric cytoskeletal fiber -namespace: cellular_component -def: "A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits." [GOC:dos] -is_a: GO:0099512 ! supramolecular fiber -intersection_of: GO:0099512 ! supramolecular fiber -intersection_of: bearer_of PATO:0015006 ! polymeric -intersection_of: part_of GO:0005856 ! cytoskeleton -relationship: part_of GO:0005856 ! cytoskeleton - [Term] id: GO:0099536 name: synaptic signaling @@ -6154,17 +5354,6 @@ def: "Cell-cell signaling in either direction across the synaptic cleft." [GOC:d subset: goslim_synapse is_a: GO:0099536 ! synaptic signaling -[Term] -id: GO:0099568 -name: cytoplasmic region -namespace: cellular_component -def: "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm." [GOC:dos] -subset: gocheck_do_not_annotate -is_a: GO:0005737 ! cytoplasm -intersection_of: GO:0005737 ! cytoplasm -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - [Term] id: GO:0110165 name: cellular anatomical entity @@ -6236,17 +5425,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2017-03-23T14:44:23Z -[Term] -id: GO:0140056 -name: organelle localization by membrane tethering -namespace: biological_process -def: "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other." [PMID:27875684] -subset: goslim_pombe -is_a: GO:0022406 ! membrane docking -is_a: GO:0051640 ! organelle localization -created_by: pg -creation_date: 2017-06-27T09:58:51Z - [Term] id: GO:0140112 name: extracellular vesicle biogenesis @@ -6274,27 +5452,6 @@ relationship: has_target_start_location GO:0005622 ! intracellular anatomical st created_by: pg creation_date: 2019-05-22T11:20:45Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1903047 name: mitotic cell cycle process @@ -6321,24 +5478,6 @@ intersection_of: part_of GO:0005576 ! extracellular region created_by: jl creation_date: 2014-10-22T14:26:11Z -[Term] -id: GO:1905349 -name: ciliary transition zone assembly -namespace: biological_process -def: "The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone." [GO_REF:0000079, GOC:cilia, GOC:TermGenie, PMID:21725307, PMID:23644468, PMID:24448408, PMID:26595381, PMID:26982032] -synonym: "cilial transition zone assembly" EXACT [GOC:TermGenie] -synonym: "cilial transition zone formation" EXACT [GOC:TermGenie] -synonym: "ciliary transition zone formation" EXACT [GOC:TermGenie] -synonym: "cilium transition zone assembly" EXACT [GOC:TermGenie] -synonym: "cilium transition zone formation" EXACT [GOC:TermGenie] -is_a: GO:0022607 ! cellular component assembly -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0035869 ! ciliary transition zone -relationship: part_of GO:0060271 ! cilium assembly -relationship: results_in_assembly_of GO:0035869 ! ciliary transition zone -created_by: pr -creation_date: 2016-08-04T14:49:43Z - [Term] id: GO:1990904 name: ribonucleoprotein complex @@ -6974,9 +6113,21 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z +[Term] +id: PATO:0002064 +name: fenestrated +namespace: quality +def: "A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes." [PATOC:me] +subset: cell_quality +subset: mpath_slim +subset: value_slim +is_a: PATO:0000141 ! structure +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X +creation_date: 2009-07-01T01:46:53Z + [Term] id: PATO:0002078 name: hollow @@ -6984,7 +6135,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6996,7 +6147,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -7007,7 +6158,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -7017,26 +6168,16 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z -[Term] -id: PATO:0002226 -name: subcylindrical -namespace: quality -def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] -subset: value_slim -is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X -creation_date: 2010-07-13T04:22:30Z - [Term] id: PATO:0002266 name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -7049,20 +6190,9 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z -[Term] -id: PATO:0002309 -name: fiber shaped -namespace: quality -def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter." [PATOC:DC] -comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). -subset: value_slim -is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X -creation_date: 2011-09-09T04:50:10Z - [Term] id: PATO:0002318 name: superelliptic @@ -7070,7 +6200,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -7083,7 +6213,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -7093,7 +6223,7 @@ namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." [PATOC:WD] subset: value_slim is_a: PATO:0015008 ! distensibility -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:48:26Z [Term] @@ -7104,7 +6234,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -7113,7 +6243,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -7175,6 +6305,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -7535,6 +6668,15 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -7574,6 +6716,18 @@ comment: Category=family. synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] is_a: PR:000000001 ! protein +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -7621,7 +6775,7 @@ xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 -xref: FBbt:00007000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 @@ -7688,7 +6842,7 @@ relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0036295 ! renal pelvis/ureter relationship: RO:0002202 UBERON:0005081 {source="GO"} ! develops from ureter ureteric bud -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -7729,7 +6883,7 @@ relationship: part_of UBERON:0001556 ! lower urinary tract relationship: RO:0002150 UBERON:0001255 ! continuous with urinary bladder relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus relationship: RO:0002202 UBERON:0013241 {source="Wikipedia"} ! develops from embryonic urethral groove -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0000058 @@ -7742,7 +6896,7 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7788,7 +6942,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7975,10 +7129,10 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle relationship: RO:0002202 UBERON:0005749 ! develops from glomerular tuft relationship: RO:0002219 UBERON:0001230 ! surrounded by glomerular capsule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:26:37Z [Term] @@ -8040,7 +7194,7 @@ xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure relationship: RO:0002202 UBERON:0002120 ! develops from pronephros -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI [Term] id: UBERON:0000081 @@ -8275,7 +7429,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -8457,7 +7611,7 @@ relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0000165 @@ -8491,7 +7645,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -8515,7 +7669,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -8596,7 +7750,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -8619,7 +7773,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -8684,11 +7838,11 @@ relationship: capable_of_part_of GO:0070295 ! renal water absorption relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -8748,7 +7902,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8783,7 +7937,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8811,7 +7965,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8836,7 +7990,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8873,7 +8027,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -8927,7 +8081,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8991,7 +8145,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -9027,7 +8181,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -9047,7 +8201,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -9074,7 +8228,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -9109,7 +8263,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -9142,7 +8296,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -9163,7 +8317,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000485 @@ -9182,7 +8336,7 @@ xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 -xref: FBbt:00007027 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007027 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 @@ -9194,7 +8348,7 @@ xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI [Term] id: UBERON:0000487 @@ -9223,7 +8377,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000489 @@ -9352,7 +8506,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -9373,7 +8527,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -9393,7 +8547,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -9427,7 +8581,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -9445,7 +8599,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -9465,7 +8619,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -9482,8 +8636,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -9509,7 +8663,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -9526,7 +8680,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -9549,7 +8703,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -9562,7 +8716,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -9579,7 +8733,7 @@ synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 -xref: FBbt:00000123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} @@ -9648,9 +8802,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -9669,7 +8823,7 @@ is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: RO:0000086 PATO:0002124 ! has quality laminar -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] @@ -9754,7 +8908,7 @@ xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 -xref: FBbt:00004857 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004857 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 @@ -9783,10 +8937,10 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0022414 ! reproductive process relationship: has_part UBERON:0000991 ! gonad relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://purl.org/dc/terms/date "2022-06-10T18:22:34Z" xsd:dateTime -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI property_value: IAO:0000116 "consider splitting genitalia from reproductive system" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-10T18:22:34Z" xsd:dateTime [Term] id: UBERON:0000991 @@ -9845,7 +8999,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9902,7 +9056,7 @@ xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 -xref: FBbt:00005056 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005056 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract @@ -9951,7 +9105,7 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -9990,7 +9144,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -10016,7 +9170,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -10044,8 +9198,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -10076,7 +9230,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -10115,7 +9269,7 @@ xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 -xref: FBbt:00005379 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005379 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 @@ -10126,7 +9280,7 @@ xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string [Term] @@ -10145,7 +9299,7 @@ xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 -xref: FBbt:00005383 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005383 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 @@ -10157,7 +9311,7 @@ xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string [Term] @@ -10175,7 +9329,7 @@ xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 -xref: FBbt:00005384 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005384 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 @@ -10188,7 +9342,7 @@ xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001045 ! midgut relationship: RO:0002202 UBERON:0003104 {source="Wikipedia"} ! develops from mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string [Term] @@ -10208,7 +9362,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -10255,7 +9409,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -10271,7 +9425,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -10288,7 +9442,7 @@ property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001072 -name: posterior vena cava +name: inferior vena cava namespace: uberon def: "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Inferior_vena_cava] subset: human_reference_atlas @@ -10296,9 +9450,8 @@ subset: pheno_slim subset: uberon_slim synonym: "caudal vena cava" RELATED [VHOG:0001194] synonym: "inferior caval vein" EXACT [http://orcid.org/0000-0002-6601-2165] -synonym: "inferior vena cava" EXACT [Wikipedia:Venae_cavae] synonym: "postcava" RELATED [] -synonym: "posterior vena cava" EXACT [Wikipedia:Venae_cavae] +synonym: "posterior vena cava" EXACT [PMID:21154280] synonym: "vena cava inferior" RELATED OMO:0003011 [BTO:0002682, Wikipedia:Inferior_vena_cava] xref: AAO:0011083 xref: BTO:0002682 @@ -10320,7 +9473,7 @@ intersection_of: UBERON:0004087 ! vena cava intersection_of: RO:0002179 UBERON:0000154 ! drains posterior region of body relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10380,10 +9533,10 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002179 UBERON:0002113 ! drains kidney -relationship: RO:0002376 UBERON:0001072 ! tributary of posterior vena cava -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002376 UBERON:0001072 ! tributary of inferior vena cava +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10420,7 +9573,7 @@ relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter relationship: RO:0002150 UBERON:0000056 {source="FMA"} ! continuous with ureter relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10451,11 +9604,11 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10493,7 +9646,7 @@ relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10535,7 +9688,7 @@ relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} ! glomerular fi relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002202 UBERON:0004199 ! develops from S-shaped body relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI [Term] id: UBERON:0001231 @@ -10629,7 +9782,7 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00047153 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00047153 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -10645,8 +9798,8 @@ is_a: UBERON:0000161 ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001555 ! digestive tract relationship: RO:0002202 UBERON:0000931 ! develops from proctodeum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10690,9 +9843,9 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10751,7 +9904,7 @@ relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney relationship: RO:0002495 UBERON:0010532 {source="Bgee:AN"} ! immediate transformation of primitive nephron -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -10791,7 +9944,7 @@ relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerul relationship: RO:0002150 UBERON:0001290 ! continuous with proximal straight tubule relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI [Term] id: UBERON:0001288 @@ -10822,7 +9975,7 @@ intersection_of: RO:0002150 UBERON:0001292 ! continuous with distal convoluted t relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule relationship: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string property_value: RO:0002175 NCBITaxon:8782 @@ -10847,7 +10000,7 @@ xref: Wikipedia:Descending_limb_of_loop_of_henle is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10911,7 +10064,7 @@ is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0004135 {source="EMAPA", source="GO", source="MA-modified-from-isa"} ! distal tubule relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10962,7 +10115,7 @@ xref: WBbt:0006919 is_a: UBERON:0000475 ! organism subdivision relationship: overlaps UBERON:0006866 ! terminal part of digestive tract relationship: RO:0002254 UBERON:0000931 ! has developmental contribution from proctodeum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/507" xsd:anyURI [Term] @@ -11023,7 +10176,7 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney relationship: RO:0002252 UBERON:0009885 ! connecting branch of interlobar artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11048,7 +10201,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -11198,7 +10351,7 @@ intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string [Term] @@ -11280,7 +10433,7 @@ is_a: UBERON:0003920 ! venous blood vessel is_a: UBERON:8410081 ! blood microvessel relationship: RO:0002176 UBERON:0001638 ! connects vein relationship: RO:0002176 UBERON:0001982 ! connects capillary -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11313,7 +10466,7 @@ intersection_of: RO:0002176 UBERON:0001982 ! connects capillary relationship: RO:0002176 UBERON:0001637 ! connects artery relationship: RO:0002176 UBERON:0001982 ! connects capillary relationship: RO:0002433 UBERON:0001637 ! contributes to morphology of artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI [Term] id: UBERON:0001981 @@ -11363,7 +10516,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11402,7 +10555,7 @@ intersection_of: RO:0002176 UBERON:0001979 ! connects venule intersection_of: RO:0002176 UBERON:0001980 ! connects arteriole relationship: RO:0002176 UBERON:0001979 ! connects venule relationship: RO:0002176 UBERON:0001980 ! connects arteriole -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string @@ -11452,7 +10605,7 @@ is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11474,7 +10627,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11553,9 +10706,9 @@ xref: XAO:0003192 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11662,7 +10815,7 @@ relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI @@ -11733,9 +10886,9 @@ relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2804-127X property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:contributor https://orcid.org/0000-0003-2804-127X [Term] id: UBERON:0002120 @@ -11872,8 +11025,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002303 @@ -11968,7 +11121,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12025,7 +11178,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12066,7 +11219,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -12129,8 +11282,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12153,7 +11306,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12351,7 +11504,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -12486,7 +11639,7 @@ relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme relationship: RO:0002202 UBERON:0000926 {source="XAO"} ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003068 @@ -12507,7 +11660,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003074 @@ -12538,7 +11691,7 @@ is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct relationship: RO:0002202 UBERON:0003060 ! develops from pronephric duct relationship: RO:0002202 UBERON:0005792 {source="EHDAA2"} ! develops from nephric ridge -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI property_value: IAO:0000116 "Consider adding subclasses for male and female specific variants" xsd:string property_value: IAO:0000116 "TODO - mesonephric portion of the nephric duct" xsd:string @@ -12575,7 +11728,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -12606,7 +11759,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -12641,7 +11794,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -12691,7 +11844,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -12747,7 +11900,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -13014,7 +12167,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -13072,10 +12225,10 @@ xref: UMLS:C0042460 {source="ncithesaurus:Vena_Cava"} xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] id: UBERON:0004100 @@ -13092,7 +12245,7 @@ xref: SCTID:279371005 xref: Wikipedia:Collecting_duct_system is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002113 ! kidney -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13416,11 +12569,11 @@ xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000362 ! renal medulla relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13581,7 +12734,7 @@ is_a: UBERON:0000485 {source="EHDAA2"} ! simple columnar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI [Term] id: UBERON:0004535 @@ -13645,8 +12798,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13740,7 +12893,7 @@ relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002178 UBERON:0001285 ! supplies nephron relationship: RO:0002252 UBERON:0004723 ! connecting branch of interlobular artery relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13789,7 +12942,7 @@ xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel disjoint_from: UBERON:0009885 {source="Wikipedia:Renal_circulation"} ! interlobar artery relationship: RO:0002170 UBERON:0001552 ! connected to kidney arcuate artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13810,7 +12963,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -13965,7 +13118,7 @@ xref: Wikipedia:Somatopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000924 ! ectoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI [Term] id: UBERON:0004875 @@ -14027,7 +13180,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14043,7 +13196,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -14183,7 +13336,7 @@ xref: Wikipedia:Descending_limb_of_loop_of_Henle is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2276" xsd:string @@ -14205,7 +13358,7 @@ xref: Wikipedia:Connecting_tubule is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0012275 ! meso-epithelium relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -14479,7 +13632,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -14660,7 +13813,7 @@ intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: capable_of GO:0003094 ! glomerular filtration relationship: part_of UBERON:0004188 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! glomerular epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI [Term] id: UBERON:0005792 @@ -14712,7 +13865,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -14741,7 +13894,7 @@ relationship: RO:0002202 UBERON:0004341 {source="Wikipedia"} ! develops from pri relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI [Term] id: UBERON:0006267 @@ -14979,7 +14132,7 @@ def: "The distalmost portion of the digestive tract, derived from the hindgut, a synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" NARROW [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] -xref: FBbt:00005756 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005756 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0005773 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002150 UBERON:0001245 ! continuous with anus @@ -15311,7 +14464,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15395,7 +14548,7 @@ relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex relationship: RO:0002202 UBERON:0010377 {source="PMID:21455939"} ! develops from mesenchyme from somatopleure relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string [Term] @@ -15548,7 +14701,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0009913 ! supplies renal lobe relationship: RO:0002178 UBERON:0009913 ! supplies renal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -15582,7 +14735,7 @@ intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: IAO:0000116 "todo - add has_part relationships." xsd:string [Term] @@ -15594,7 +14747,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -15731,8 +14884,8 @@ is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002328 GO:0040011 ! functionally related to locomotion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-04-23T10:46:51Z [Term] @@ -15836,7 +14989,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -16229,7 +15382,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -16382,8 +15535,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Typedef] id: BFO:0000067 @@ -17453,8 +16606,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17462,8 +16615,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17472,8 +16625,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -17624,16 +16777,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -17642,6 +16799,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -17659,6 +16817,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -17877,6 +17036,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -18335,18 +17495,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/src/ontology/subsets/kidney_upper_slim.owl b/src/ontology/subsets/kidney_upper_slim.owl index d55f2848a..06b276c12 100644 --- a/src/ontology/subsets/kidney_upper_slim.owl +++ b/src/ontology/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4511,6 +4517,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4522,6 +4530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4532,6 +4541,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4544,6 +4554,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4562,6 +4573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4591,6 +4603,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4699,6 +4712,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4710,6 +4724,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4721,6 +4736,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -5504,49 +5520,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A cell that has a filiform extrusion of the cell surface. - VHOG:0001532 - XAO:0000031 - ZFA:0009032 - - ciliated cell - - - - - A cell that has a filiform extrusion of the cell surface. - GOC:tfm - - - - - ZFA:0009032 - - - - - @@ -5596,43 +5569,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - An epithelial cell that has a cilia. - FMA:70605 - ZFA:0009035 - - ciliated epithelial cell - - - - - An epithelial cell that has a cilia. - GOC:tfm - - - - - ZFA:0009035 - - - - - @@ -5680,15 +5616,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - @@ -5705,17 +5640,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -5841,7 +5769,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -6477,23 +6410,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - ZFA:0009143 - brush border epithelial cell - - - - - ZFA:0009143 - - - - - @@ -8009,12 +7925,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + + + + + + + + + + + + + + An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. ZFA:0009286 window cell - fenestrated cell + fenestrated endothelial cell + + + + An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. + DOI:10.1007/978-3-211-99390-3_133 + @@ -8754,7 +8694,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -8797,7 +8737,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -8836,7 +8776,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -8880,7 +8820,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Epithelial cell derived from mesoderm or mesenchyme. - 2010-06-29T03:49:14Z + 2010-06-29T03:49:14Z FMA:69076 ZFA:0009388 epithelial mesenchymal cell @@ -8908,7 +8848,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -8954,7 +8894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. - 2010-08-25T02:20:55Z + 2010-08-25T02:20:55Z FMA:84143 KUPO:0001033 Goormaghtigh cell @@ -8993,24 +8933,23 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + + + + + + An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. - 2010-08-26T10:59:44Z + 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 glomerular endothelial cell - - - - - true - @@ -9044,7 +8983,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -9117,7 +9056,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -9135,6 +9073,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. epithelial cell of proximal tubule @@ -9176,7 +9115,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -9215,7 +9154,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -9245,7 +9184,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -9290,7 +9229,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -9326,7 +9265,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell of the kidney. - 2011-02-08T10:46:34Z + 2011-02-08T10:46:34Z KUPO:0001019 ZFA:0009374 @@ -9360,7 +9299,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -9444,7 +9383,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of a cortex of kidney. - 2011-10-25T03:49:41Z + 2011-10-25T03:49:41Z kidney cortical cell @@ -9493,7 +9432,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -9765,7 +9704,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -9801,7 +9740,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -9836,7 +9775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -10321,12 +10260,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney corpuscule cell - - - - - true - @@ -10484,12 +10417,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different KUPO:0001036 glomerular cell - - - - - true - @@ -10602,7 +10529,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -11011,59 +10937,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. - https://github.com/geneontology/go-ontology/issues/23114 - https://github.com/geneontology/go-ontology/issues/23195 - microtubule cytoskeleton organisation - biological_process - microtubule cytoskeleton organization and biogenesis - GO:0000226 - - microtubule cytoskeleton organization - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. - GOC:mah - - - - - microtubule cytoskeleton organisation - GOC:mah - - - - - microtubule cytoskeleton organization and biogenesis - GOC:mah - - - - @@ -11116,7 +10989,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 - Reactome:69278 @@ -11240,37 +11112,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - A process that results in a parallel arrangement of microtubules. - microtubule bundling - biological_process - GO:0001578 - microtubule bundle formation - - - - - A process that results in a parallel arrangement of microtubules. - GOC:dph - - - - @@ -12321,32 +12162,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12652,132 +12493,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. - Wikipedia:Vacuole - cellular_component - vacuolar carboxypeptidase Y - GO:0005773 - - - - - - - - - - - - - vacuole - - - - - A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. - GOC:mtg_sensu - ISBN:0198506732 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. - Golgi - NIF_Subcellular:sao451912436 - Wikipedia:Golgi_apparatus - Golgi complex - Golgi ribbon - cellular_component - GO:0005794 - - - - - - - - - - - - Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. - Golgi apparatus - - - - - A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. - ISBN:0198506732 - - - - - - - - - Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. - NIF_Subcellular:sao819927218 - cellular_component - Golgi vesicle - vesicular component - GO:0005798 - Note that this definition includes vesicles that are transiently associated with the Golgi. - Golgi-associated vesicle - - - - - Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. - GOC:mah - - - - - vesicular component - NIF_Subcellular:sao138219748 - - - - @@ -12837,76 +12552,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. - Wikipedia:Cytoskeleton - cellular_component - GO:0005856 - - - - - - - - - - - - - - cytoskeleton - - - - - A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. - GOC:mah - PMID:16959967 - PMID:27419875 - - - - - - - - - - - - - - - Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. - NIF_Subcellular:sao1846835077 - Wikipedia:Microtubule - microtubuli - microtubulus - neurotubule - cellular_component - GO:0005874 - - microtubule - - - - - Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. - ISBN:0879693568 - - - - - neurotubule - NIF_Subcellular:sao248349196 - - - - @@ -13005,116 +12650,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. - - - - - - - GO:0072372 - FMA:67181 - NIF_Subcellular:sao787716553 - Wikipedia:Cilium - eukaryotic flagellum - microtubule-based flagellum - primary cilium - cellular_component - flagellum - GO:0005929 - - - - - Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. - cilium - - - - - A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. - GOC:cilia - GOC:curators - GOC:kmv - GOC:vw - ISBN:0198547684 - PMID:16824949 - PMID:17009929 - PMID:20144998 - - - - - - - - - - - - - - - - - - - - - - - - - - - The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GO:0035085 - GO:0035086 - Wikipedia:Axoneme - ciliary axoneme - cilium axoneme - flagellar axoneme - flagellum axoneme - cellular_component - GO:0005930 - - Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. - axoneme - - - - - The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GOC:bf - GOC:cilia - ISBN:0198547684 - - - - @@ -13351,37 +12886,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. - biological_process - GO:0006903 - vesicle targeting - - - - - The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. - GOC:mah - PMID:17335816 - - - - @@ -13595,123 +13099,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. - cytoskeleton organisation - biological_process - cytoskeletal organization and biogenesis - cytoskeletal regulator activity - cytoskeleton organization and biogenesis - GO:0007010 - - - - - - - cytoskeleton organization - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. - GOC:dph - GOC:jl - GOC:mah - - - - - cytoskeletal organization and biogenesis - GOC:mah - - - - - cytoskeleton organization and biogenesis - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. - https://github.com/geneontology/go-ontology/issues/19809 - biological_process - GO:0007017 - - microtubule-based process - - - - - Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. - GOC:mah - - - - - - - - - A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - biological_process - GO:0007018 - - - microtubule-based movement - - - - - A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - GOC:cjm - ISBN:0815316194 - - - - @@ -14461,7 +13848,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -14828,56 +14214,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. - tb - 2009-05-27T10:56:08Z - microtubule-based transport - establishment of localization by movement along microtubule - movement along microtubule - biological_process - GO:0010970 - transport along microtubule - - - - - The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. - GOC:dph - GOC:mah - GOC:tb - - - - - establishment of localization by movement along microtubule - GOC:dph - - - - @@ -14934,46 +14270,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. - Wikipedia:Endomembrane_system - cellular_component - GO:0012505 - - - - endomembrane system - - - - - A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. - GOC:lh - - - - @@ -14988,8 +14284,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + - The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport @@ -15009,25 +14305,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. - cellular_component - GO:0015630 - microtubule cytoskeleton - - - - - The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. - GOC:jl - ISBN:0395825172 - - - - @@ -15225,64 +14502,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. - https://github.com/geneontology/go-ontology/issues/25421 - GO:0006899 - vesicle transport - vesicular transport - nonselective vesicle transport - biological_process - protein sorting along secretory pathway - vesicle trafficking - GO:0016192 - - - - - - - - vesicle-mediated transport - - - - - A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. - GOC:ai - GOC:mah - ISBN:08789310662000 - - - - - vesicular transport - GOC:mah - - - - @@ -15575,26 +14794,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere. - biological_process - GO:0022406 - - membrane docking - - - - - The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere. - GOC:isa_complete - PMID:27875684 - - - - @@ -15960,7 +15159,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -16012,7 +15211,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:18391171 @@ -16047,7 +15246,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -16416,76 +15614,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. - biological_process - GO:0030705 - - - cytoskeleton-dependent intracellular transport - - - - - The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. - GOC:mah - - - - - - - - - - - - - - - A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. - intraflagellar transport complex - intraflagellar transport particle - cellular_component - IFT complex - GO:0030990 - - Note that we deem cilia and microtubule-based flagella to be equivalent. - intraciliary transport particle - - - - - A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. - GOC:cilia - GOC:kmv - PMID:14570576 - PMID:22118932 - PMID:23945166 - - - - @@ -16522,110 +15650,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A vesicle found in the cytoplasm of a cell. - GO:0016023 - NIF_Subcellular:sao180601769 - cellular_component - cytoplasmic membrane bounded vesicle - cytoplasmic membrane-enclosed vesicle - cytoplasmic, membrane-bounded vesicle - GO:0031410 - - - - - - - cytoplasmic vesicle - - - - - A vesicle found in the cytoplasm of a cell. - GOC:ai - GOC:mah - GOC:vesicles - - - - - - - - - - - - - - - - - - - - - - - - - - A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. - https://github.com/geneontology/go-ontology/issues/22021 - GO:0034629 - establishment and maintenance of protein complex localization - protein complex localisation - biological_process - cellular protein complex localisation - cellular protein complex localization - cellular protein-containing complex localization - establishment and maintenance of cellular protein complex localization - protein complex localization - GO:0031503 - protein-containing complex localization - - - - - A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. - GOC:mah - - - - - protein complex localisation - GOC:mah - - - - - cellular protein complex localisation - GOC:mah - - - - @@ -16856,42 +15880,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. - cellular_component - GO:0032838 - plasma membrane bounded cell projection cytoplasm - - - - - All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. - GOC:krc - GOC:mah - - - - @@ -17049,55 +16037,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A process in which a protein is transported to, or maintained in, a location within an organelle. - protein localisation to organelle - protein localization in organelle - biological_process - GO:0033365 - protein localization to organelle - - - - - A process in which a protein is transported to, or maintained in, a location within an organelle. - GOC:mah - - - - - protein localisation to organelle - GOC:mah - - - - - protein localization in organelle - GOC:mah - - - - @@ -17181,72 +16120,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GO:0035083 - GO:0035084 - ciliary axoneme assembly - cilium axoneme assembly - flagellar axoneme assembly - flagellum axoneme assembly - biological_process - axoneme biogenesis - cilium axoneme biogenesis - GO:0035082 - Note that cilia and eukaryotic flagella are deemed to be equivalent. - axoneme assembly - - - - - The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GOC:bf - GOC:cilia - GOC:jl - ISBN:0815316194 - - - - - axoneme biogenesis - GOC:mah - - - - - cilium axoneme biogenesis - GOC:mah - - - - @@ -17428,81 +16301,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. - bf - 2011-03-17T10:55:42Z - intraflagellar transport - Reactome:R-HSA-5620924.2 - biological_process - intraciliary transport involved in cilium morphogenesis - intraflagellar transport involved in cilium morphogenesis - GO:0035735 - intraciliary transport involved in cilium assembly - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. - GOC:bf - GOC:cilia - Reactome:R-HSA-5620924.2 - - - - - - - - - - - - - - - A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. - bf - 2011-05-25T03:09:58Z - cilial transition zone - cilium transition zone - cellular_component - connecting cilium - GO:0035869 - Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone. - ciliary transition zone - - - - - A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. - GOC:cilia - GOC:kmv - PMID:21422230 - - - - @@ -17568,86 +16366,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. - - - - - - - GO:0035734 - Wikipedia:Intraflagellar_transport - intraflagellar transport - intraflagellar transport involved in cilium organization - intraflagellar transport involved in microtubule-based flagellum organisation - biological_process - IFT - GO:0042073 - Note that we deem cilium and microtubule-based flagellum to be equivalent. - intraciliary transport - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. - GOC:cilia - GOC:kmv - PMID:17981739 - PMID:18180368 - PMID:22869374 - Reactome:R-HSA-5620924.2 - - - - @@ -17735,7 +16453,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -18278,6 +16996,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite primary metabolism biological_process GO:0044238 @@ -18293,7 +17012,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators - http://www.metacyc.org @@ -18324,61 +17042,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - jl - 2013-03-27T15:09:58Z - microtubule-based flagellum organization - biological_process - GO:0044782 - - - Note that we deem cilium and microtubule-based flagellum to be equivalent. - cilium organization - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - GOC:cilia - GOC:jl - - - - @@ -18484,54 +17147,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances within a cell. - jl - 2013-12-18T14:04:50Z - GO:1902582 - biological_process - single organism intracellular transport - single-organism intracellular transport - GO:0046907 - intracellular transport - - - - - The directed movement of substances within a cell. - GOC:ai - - - - - single organism intracellular transport - GOC:TermGenie - - - - @@ -18569,102 +17184,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. - biological_process - Golgi-derived vesicle transport - GO:0048193 - - Golgi vesicle transport - - - - - The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. - GOC:jid - ISBN:0716731363 - PMID:10219233 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. - Golgi vesicle targeting - dictyosome vesicle targeting - vesicle targeting, to, from or within dictyosome - biological_process - GO:0048199 - vesicle targeting, to, from or within Golgi - - - - - The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. - GOC:jid - GOC:mah - ISBN:0716731363 - PMID:10219233 - - - - @@ -19616,63 +18135,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process in which an organelle is transported to, and/or maintained in, a specific location. - https://github.com/geneontology/go-ontology/issues/19809 - establishment and maintenance of organelle localization - organelle localisation - biological_process - GO:0051640 - - organelle localization - - - - - Any process in which an organelle is transported to, and/or maintained in, a specific location. - GOC:ai - - - - - organelle localisation - GOC:mah - - - - @@ -19719,199 +18181,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - cytoplasmic vesicle localization - establishment and maintenance of vesicle localization - vesicle localisation - biological_process - GO:0051648 - vesicle localization - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - GOC:ai - - - - - vesicle localisation - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. - establishment of localisation in cell - establishment of intracellular localization - establishment of localization within cell - positioning within cell - biological_process - establishment of cellular localization - GO:0051649 - establishment of localization in cell - - - - - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. - GOC:ai - GOC:dos - GOC:dph - GOC:tb - - - - - establishment of localisation in cell - GOC:mah - - - - - establishment of cellular localization - GOC:dph - GOC:tb - - - - - - - - - - - - - - - - - - - - - - The directed movement of a vesicle to a specific location. - establishment of vesicle localisation - biological_process - GO:0051650 - establishment of vesicle localization - - - - - The directed movement of a vesicle to a specific location. - GOC:ai - - - - - establishment of vesicle localisation - GOC:mah - - - - - - - - - - - - - - - - - - - - - The directed movement of an organelle to a specific location. - establishment of organelle localisation - biological_process - GO:0051656 - establishment of organelle localization - - - - - The directed movement of an organelle to a specific location. - GOC:ai - - - - - establishment of organelle localisation - GOC:mah - - - - @@ -20005,121 +18274,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - - - - - - - GO:0042384 - Reactome:R-HSA-5617833.2 - ciliogenesis - cilium formation - microtubule-based flagellum assembly - biological_process - cilium biogenesis - cilium morphogenesis - cilium organization - GO:0060271 - Note that we deem cilium and microtubule-based flagellum to be equivalent. - cilium assembly - - - - - The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - GOC:BHF - GOC:cilia - GOC:dph - GOC:kmv - GOC:pr - GOC:vw - ISBN:0198506732 - PMID:13978319 - PMID:27350441 - Reactome:R-HSA-5617833.2 - - - - - cilium biogenesis - GOC:mah - - - - - cilium organization - GOC:dph - - - - @@ -20216,61 +18370,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process in which a protein is transported to, or maintained in, a location within a cilium. - - - - - - - dph - 2013-03-22T15:41:44Z - biological_process - GO:0061512 - protein localization to cilium - - - - - A process in which a protein is transported to, or maintained in, a location within a cilium. - GOC:dph - - - - @@ -20727,51 +18826,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. - mah - 2010-03-08T02:15:14Z - biological_process - GO:0071702 - organic substance transport - - - - - The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. - GOC:mah - - - - - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism - biological_process - GO:0071704 - - organic substance metabolic process - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - GOC:mah - - - - @@ -20992,55 +19046,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. - pr - 2011-03-23T01:52:31Z - cilium plasm - microtubule-based flagellar matrix - microtubule-based flagellum matrix - cellular_component - cilial cytoplasm - ciliary cytoplasm - cilium cytoplasm - microtubule-based flagellar cytoplasm - microtubule-based flagellum cytoplasm - GO:0097014 - Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". - ciliary plasm - - - - - All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. - GOC:BHF - GOC:cilia - GOC:dos - PMID:17895364 - - - - @@ -21157,139 +19162,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - An arrangement of closely apposed microtubules running parallel to each other. - pr - 2012-11-07T15:01:27Z - NIF_Subcellular:sao1872343973 - microtubule fascicle - cellular_component - GO:0097427 - microtubule bundle - - - - - An arrangement of closely apposed microtubules running parallel to each other. - NIF_Subcellular:sao1872343973 - - - - - - - - - - - - - - - - - - - - - Any vesicle that is part of the intracellular region. - pr - 2016-03-29T17:39:45Z - cellular_component - GO:0097708 - intracellular vesicle - - - - - Any vesicle that is part of the intracellular region. - GOC:vesicles - - - - - - - - - - - - - - - The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane. - pr - 2016-08-05T16:12:33Z - Reactome:R-HSA-5620912.1 - ciliary basal body docking - biological_process - anchoring of the basal body to the plasma membrane - GO:0097711 - Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella. - ciliary basal body-plasma membrane docking - - - - - The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane. - GOC:cilia - PMID:13978319 - PMID:23348840 - PMID:23530209 - PMID:25686250 - PMID:26981235 - Reactome:R-HSA-5620912.1 - - - - - - - - - - - - - - - The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. - pr - 2016-08-05T16:16:28Z - biological_process - GO:0097712 - vesicle targeting, trans-Golgi to periciliary membrane compartment - - - - - The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. - GOC:cilia - PMID:20106869 - PMID:23351793 - PMID:24814148 - PMID:26485645 - Reactome:R-HSA-5620920.1 - - - - @@ -21689,122 +19561,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - biological_process - GO:0099111 - microtubule-based transport - - - - - A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - GOC:cjm - ISBN:0815316194 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GO:0043205 - cellular_component - fibril - GO:0099512 - supramolecular fiber - - - - - A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. - cellular_component - GO:0099513 - polymeric cytoskeletal fiber - - - - - A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. - GOC:dos - - - - @@ -21873,42 +19629,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. - cellular_component - GO:0099568 - - cytoplasmic region - - - - - Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. - GOC:dos - - - - @@ -22095,28 +19815,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other. - pg - 2017-06-27T09:58:51Z - biological_process - GO:0140056 - - organelle localization by membrane tethering - - - - - The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other. - PMID:27875684 - - - - @@ -22188,63 +19886,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -22327,91 +19968,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. - pr - 2016-08-04T14:49:43Z - cilial transition zone assembly - cilial transition zone formation - ciliary transition zone formation - cilium transition zone assembly - cilium transition zone formation - biological_process - GO:1905349 - ciliary transition zone assembly - - - - - The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. - GOC:TermGenie - GOC:cilia - GO_REF:0000079 - PMID:21725307 - PMID:23644468 - PMID:24448408 - PMID:26595381 - PMID:26982032 - - - - - cilial transition zone assembly - GOC:TermGenie - - - - - cilial transition zone formation - GOC:TermGenie - - - - - ciliary transition zone formation - GOC:TermGenie - - - - - cilium transition zone assembly - GOC:TermGenie - - - - - cilium transition zone formation - GOC:TermGenie - - - - @@ -23883,6 +21439,29 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes. + + 2009-07-01T01:46:53Z + quality + PATO:0002064 + + + + fenestrated + + + + + A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes. + PATOC:me + + + + @@ -23970,27 +21549,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. - - 2010-07-13T04:22:30Z - quality - PATO:0002226 - - subcylindrical - - - - - A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. - url:http://www.thefreedictionary.com/Subcylindrical - - - - @@ -24035,28 +21593,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. - - 2011-09-09T04:50:10Z - quality - PATO:0002309 - - Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). - fiber shaped - - - - - A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. - PATOC:DC - - - - @@ -24275,6 +21811,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -25226,6 +22770,39 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -25357,6 +22934,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -25552,7 +23181,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25606,14 +23235,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -25663,7 +23292,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25711,14 +23340,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -26225,7 +23854,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26275,14 +23904,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -26545,14 +24174,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -26584,24 +24213,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different metanephros - + - + - + GO - + ISBN:9780878932504 @@ -26716,8 +24345,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -26741,11 +24370,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureteric bud - + - + @@ -26758,13 +24387,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 - + ISBN:9780878932504 @@ -27145,7 +24774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27181,14 +24810,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -27448,8 +25077,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -27475,24 +25104,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -27533,8 +25162,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -27552,24 +25181,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -27592,7 +25221,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27631,14 +25260,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -27920,15 +25549,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -27965,34 +25594,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -29334,7 +26963,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29376,14 +27005,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -29741,7 +27370,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29776,14 +27405,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different abdomen - + - + MA @@ -30012,7 +27641,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -30047,14 +27676,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -30094,7 +27723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -30129,14 +27758,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -30177,7 +27806,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -30218,14 +27847,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -30391,7 +28020,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30434,7 +28063,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -30447,7 +28076,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -30509,7 +28138,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30581,14 +28210,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -31442,7 +29071,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31492,14 +29121,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -31565,7 +29194,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -31610,7 +29239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -31624,7 +29253,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -31821,7 +29450,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31855,14 +29484,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -32142,7 +29771,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0000388 galen:InferiorVenaCava inferior caval vein - inferior vena cava posterior vena cava uberon caudal vena cava @@ -32152,7 +29780,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - posterior vena cava + inferior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png @@ -32174,17 +29802,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different inferior caval vein http://orcid.org/0000-0002-6601-2165 - - - - inferior vena cava - Wikipedia:Venae_cavae - posterior vena cava - Wikipedia:Venae_cavae + PMID:21154280 @@ -32360,14 +29982,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32419,24 +30041,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -32482,7 +30104,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32518,14 +30140,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -32561,7 +30183,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32606,14 +30228,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -32687,7 +30309,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32729,14 +30351,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -32826,10 +30448,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32873,7 +30495,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron tubule - + @@ -32882,14 +30504,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + GO MA ZFA @@ -32903,7 +30525,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -33117,7 +30739,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33164,7 +30786,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -33177,7 +30799,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -33307,7 +30929,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33320,7 +30942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -33351,24 +30973,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -33419,14 +31041,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33462,11 +31084,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -33479,13 +31101,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GO - + Wikipedia @@ -33617,7 +31239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33644,7 +31266,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -33657,7 +31279,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -33681,14 +31303,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33727,11 +31349,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal straight tubule - + - + @@ -33744,13 +31366,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + MA - + MA @@ -33792,7 +31414,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33828,7 +31450,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -33841,7 +31463,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EMAPA GO MA-modified-from-isa @@ -34116,7 +31738,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34139,14 +31761,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -34187,7 +31809,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -34224,14 +31846,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -34867,8 +32489,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -34881,7 +32503,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34935,34 +32557,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35819,7 +33441,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35871,14 +33493,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney - + - + FMA @@ -35913,8 +33535,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -35952,11 +33574,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -35969,13 +33591,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + ZFA @@ -36302,7 +33924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36321,7 +33943,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -36343,24 +33965,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different juxtaglomerular apparatus - + - + - + MA - + GO @@ -36484,8 +34106,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -36502,24 +34124,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -36661,9 +34283,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -36711,15 +34333,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -36738,19 +34360,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36790,8 +34412,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -36829,11 +34451,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -36846,13 +34468,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -36912,8 +34534,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -36931,24 +34553,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different macula densa - + - + - + MA - + GO @@ -36973,22 +34595,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37021,45 +34643,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37423,7 +35045,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37476,14 +35098,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -37701,7 +35323,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -37724,14 +35346,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -37772,8 +35394,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -37792,11 +35414,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -37809,13 +35431,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Wikipedia - + XAO @@ -37921,9 +35543,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -37962,34 +35584,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -38098,7 +35720,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -38127,7 +35749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -38140,7 +35762,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -38194,9 +35816,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38225,34 +35847,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38292,7 +35914,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38318,7 +35940,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38331,7 +35953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -38378,7 +36000,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38418,7 +36040,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38431,7 +36053,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -38481,15 +36103,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -38506,15 +36128,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -38527,19 +36149,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -38568,8 +36190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -38593,11 +36215,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -38616,13 +36238,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -38867,7 +36489,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38893,14 +36515,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -39588,7 +37210,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -39603,14 +37225,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -40190,8 +37812,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -40208,24 +37830,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal tubule - + - + - + GO - + GO @@ -40284,7 +37906,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -40294,14 +37916,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004136 intermediate tubule - + - + FMA @@ -40377,8 +37999,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -40390,24 +38012,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -40460,7 +38082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -40479,14 +38101,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -40708,8 +38330,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -40719,24 +38341,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different comma-shaped body - + - + - + cjm - + ZFA @@ -40758,8 +38380,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -40771,24 +38393,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different S-shaped body - + - + - + cjm - + GO @@ -41200,7 +38822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41238,14 +38860,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -41785,7 +39407,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41822,14 +39444,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -42189,7 +39811,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42203,14 +39825,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -42237,7 +39859,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42276,14 +39898,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -42581,7 +40203,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42602,14 +40224,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -42675,9 +40297,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -42697,34 +40319,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -43199,7 +40821,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -43207,14 +40829,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005095 kidney rudiment - + - + GO @@ -43330,7 +40952,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -43348,14 +40970,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -44086,7 +41708,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44102,14 +41724,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -44226,7 +41848,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44244,14 +41866,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -44279,7 +41901,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44306,7 +41928,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different gonad primordium - + @@ -44319,7 +41941,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -44378,14 +42000,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -44403,24 +42025,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -44467,7 +42089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44484,14 +42106,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular tuft - + - + Wikipedia @@ -44741,7 +42363,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44769,14 +42391,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -44861,7 +42483,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44871,7 +42493,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -44890,7 +42512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -44987,7 +42609,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45026,14 +42648,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -45067,7 +42689,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -45081,7 +42703,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -45094,7 +42716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45122,7 +42744,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -45139,14 +42761,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45690,7 +43312,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -45700,14 +43322,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0006853 renal cortex tubule - + - + MA @@ -46379,7 +44001,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46405,7 +44027,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -46421,7 +44043,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -46582,7 +44204,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46590,7 +44212,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -46603,7 +44225,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -46817,7 +44439,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46834,14 +44456,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -46979,7 +44601,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47017,14 +44639,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -47077,7 +44699,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -47088,7 +44710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0008987 renal parenchyma - + @@ -47101,7 +44723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -47171,7 +44793,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47188,14 +44810,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47314,7 +44936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47322,14 +44944,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47428,7 +45050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47438,14 +45060,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -47766,7 +45388,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47784,14 +45406,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010227 future cardiac atrium - + - + ZFA @@ -47934,7 +45556,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47948,7 +45570,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010377 mesenchyme from somatopleure - + @@ -47961,7 +45583,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -47977,7 +45599,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -47987,14 +45609,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -48027,7 +45649,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48043,7 +45665,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010532 primitive nephron - + @@ -48056,7 +45678,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -48072,7 +45694,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48083,7 +45705,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010536 nephron progenitor - + @@ -48096,7 +45718,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -48339,8 +45961,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -48352,11 +45974,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -48369,13 +45991,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -48436,7 +46058,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48446,7 +46068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48459,7 +46081,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -48483,7 +46105,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48508,14 +46130,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different upper urinary tract - + - + FMA @@ -48833,7 +46455,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48848,14 +46470,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -48878,20 +46500,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -48901,20 +46523,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -48941,7 +46563,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48961,14 +46583,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeleton of pelvic complex - + - + FMA @@ -49020,7 +46642,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -49031,14 +46653,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -49609,7 +47231,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -49632,7 +47254,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -49645,7 +47267,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -50056,7 +47678,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -50067,14 +47689,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis/ureter - + - + NCIT @@ -50419,5 +48041,5 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + diff --git a/src/ontology/subsets/kidney_upper_slim.tsv b/src/ontology/subsets/kidney_upper_slim.tsv index 1147052a5..684848508 100644 --- a/src/ontology/subsets/kidney_upper_slim.tsv +++ b/src/ontology/subsets/kidney_upper_slim.tsv @@ -1,364 +1,332 @@ ?x ?label -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1002 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1008 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1014 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1021 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1026 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1031 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1037 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1042 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+_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid875 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid881 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid890 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid896 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid905 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid912 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid925 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid937 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid943 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid949 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid955 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid961 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid967 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid973 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid980 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid988 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -372,9 +340,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "non-terminally differentiated cell" "myoblast" "fibroblast" - "ciliated cell" "epithelial cell" - "ciliated epithelial cell" "duct epithelial cell" "blood vessel endothelial cell" "non-branched duct epithelial cell" @@ -397,7 +363,6 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "mesodermal cell" "endodermal cell" "erythrocyte" - "brush border epithelial cell" "eukaryotic cell" "oxygen accumulating cell" "migratory neural crest cell" @@ -420,7 +385,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "supporting cell" "kidney granular cell" "mesangial cell" - "fenestrated cell" + "fenestrated endothelial cell" "pericyte" "muscle precursor cell" "somatic stem cell" @@ -492,13 +457,11 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "renal interstitial pericyte" "interstitial cell" "perivascular cell" - "microtubule cytoskeleton organization" "mitotic cell cycle" "nuclear division" "chromatin" "heterochromatin" "action potential" - "microtubule bundle formation" "formation of translation initiation ternary complex" "formation of primary germ layer" "ectoderm formation" @@ -540,16 +503,9 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "chromosome" "nucleolus" "cytoplasm" - "vacuole" - "Golgi apparatus" - "Golgi-associated vesicle" "ribosome" - "cytoskeleton" - "microtubule" "plasma membrane" "cell-cell junction" - "cilium" - "axoneme" "translation" "translational initiation" "translational elongation" @@ -557,14 +513,10 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "transport" "monoatomic ion transport" "water transport" - "vesicle targeting" "apoptotic process" "cellular component disassembly involved in execution phase of apoptosis" "muscle contraction" "organelle organization" - "cytoskeleton organization" - "microtubule-based process" - "microtubule-based movement" "cell cycle" "endomitotic cell cycle" "cell communication" @@ -597,17 +549,13 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "tissue development" "cellular process" "gene expression" - "transport along microtubule" "programmed cell death" - "endomembrane system" "protein transport" - "microtubule cytoskeleton" "gas transport" "oxygen transport" "membrane" "cellular component organization" "vesicle organization" - "vesicle-mediated transport" "morphogenesis of embryonic epithelium" "cell migration" "stem cell division" @@ -616,7 +564,6 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "sexual reproduction" "neural tube development" "cell cycle process" - "membrane docking" "cellular component disassembly" "reproductive process" "digestive system process" @@ -637,11 +584,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "apoptotic nuclear changes" "apoptotic chromosome condensation" "external encapsulating structure" - "cytoskeleton-dependent intracellular transport" - "intraciliary transport particle" "extracellular matrix" - "cytoplasmic vesicle" - "protein-containing complex localization" "membrane-enclosed lumen" "nuclear lumen" "vesicle" @@ -649,26 +592,20 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "bleb assembly" "multicellular organismal process" "developmental process" - "plasma membrane bounded cell projection cytoplasm" "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" "protein-DNA complex" "macromolecule localization" - "protein localization to organelle" "erythrocyte homeostasis" "monoatomic ion transmembrane transport" - "axoneme assembly" "tube formation" "tube morphogenesis" "tube development" "establishment of protein localization to extracellular region" - "intraciliary transport involved in cilium assembly" - "ciliary transition zone" "locomotion" "embryonic cleavage" "fluid transport" - "intraciliary transport" "regulation of membrane potential" "homeostatic process" "cell projection" @@ -690,14 +627,10 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "cellular metabolic process" "primary metabolic process" "cellular biosynthetic process" - "cilium organization" "establishment of protein localization" "synapse" "secretion" - "intracellular transport" "somatic stem cell division" - "Golgi vesicle transport" - "vesicle targeting, to, from or within Golgi" "organelle fission" "mesoderm morphogenesis" "cell development" @@ -725,20 +658,13 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "regulation of multicellular organismal process" "chromosome organization" "cell division" - "organelle localization" "cellular localization" - "vesicle localization" - "establishment of localization in cell" - "establishment of vesicle localization" - "establishment of organelle localization" "cellular response to stimulus" "transmembrane transport" "micturition" - "cilium assembly" "epithelium development" "epithelial tube morphogenesis" "morphogenesis of a branching epithelium" - "protein localization to cilium" "collagen-containing extracellular matrix" "protein-containing complex assembly" "biological regulation" @@ -752,22 +678,15 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "cellular macromolecule localization" "organelle assembly" "protein localization to extracellular region" - "organic substance transport" - "organic substance metabolic process" "protein-RNA complex organization" "cellular component organization or biogenesis" "cell periphery" "extracellular exosome assembly" "epithelial tube formation" - "ciliary plasm" "apoptotic signaling pathway" "execution phase of apoptosis" "renal filtration" "renal tubular secretion" - "microtubule bundle" - "intracellular vesicle" - "ciliary basal body-plasma membrane docking" - "vesicle targeting, trans-Golgi to periciliary membrane compartment" "extracellular exosome biogenesis" "plasma membrane region" "network-forming collagen trimer" @@ -780,24 +699,17 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "anterograde trans-synaptic signaling" "supramolecular complex" "supramolecular polymer" - "microtubule-based transport" - "supramolecular fiber" - "polymeric cytoskeletal fiber" "synaptic signaling" "trans-synaptic signaling" - "cytoplasmic region" "cellular anatomical entity" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" "mitotic nuclear division" - "organelle localization by membrane tethering" "extracellular vesicle biogenesis" "export from cell" - "organic substance biosynthetic process" "mitotic cell cycle process" "extracellular vesicle" - "ciliary transition zone assembly" "ribonucleoprotein complex" "root" "Muridae" @@ -864,14 +776,13 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "structure, cavities" "biconcave" "dendritic" + "fenestrated" "hollow" "basophilic" "laminar" "quality of a substance" - "subcylindrical" "3-D shape" "tubular" - "fiber shaped" "superelliptic" "acidophilic" "distensible" @@ -911,10 +822,12 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "renin" "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "eukaryotic protein" "angiotensinogenase" + "protein-containing molecular entity" "processual entity" "tube" "appendage" @@ -1004,7 +917,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "primordium" "neural tube" "anatomical entity" - "posterior vena cava" + "inferior vena cava" "urine" "renal vein" "renal pelvis" diff --git a/subsets/blood_and_immune_upper_slim.json b/subsets/blood_and_immune_upper_slim.json index bb7421769..7c2d36189 100644 --- a/subsets/blood_and_immune_upper_slim.json +++ b/subsets/blood_and_immune_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -661,10 +508,6 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cuboidal endothelial cell of vascular tree" - } ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -3313,32 +3156,6 @@ "val" : "2010-06-29T03:38:22Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002078", - "lbl" : "meso-epithelial cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Epithelial cell derived from mesoderm or mesenchyme.", - "xrefs" : [ "FMA:69076", "GOC:tfm" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial mesenchymal cell" - } ], - "xrefs" : [ { - "val" : "FMA:69076" - }, { - "val" : "ZFA:0009388" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-06-29T03:49:14Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002087", "lbl" : "nongranular leukocyte", @@ -3971,7 +3788,7 @@ "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://www.wikidata.org/entity/Q35563349" + "val" : "http://www.wikidata.org/entity/Q35563349" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-02-11T17:29:04Z" @@ -3992,62 +3809,6 @@ "val" : "2022-11-04T14:40:00Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -4055,7 +3816,7 @@ "meta" : { "definition" : { "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", - "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + "xrefs" : [ "GOC:mah", "ISBN:0815316194" ] }, "comments" : [ "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -5923,7 +5684,7 @@ "meta" : { "definition" : { "val" : "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.", - "xrefs" : [ "GOC:bf", "Wikipedia:GPCR", "http://www.iuphar-db.org" ] + "xrefs" : [ "GOC:bf", "Wikipedia:GPCR" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], "synonyms" : [ { @@ -6795,7 +6556,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", + "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", "xrefs" : [ "GOC:mah", "ISBN:0716731363", "PMID:22323285" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -8936,7 +8697,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -8966,7 +8727,7 @@ "meta" : { "definition" : { "val" : "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:18391171" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", @@ -8988,7 +8749,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -10838,7 +10599,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -11250,13 +11011,16 @@ "meta" : { "definition" : { "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", - "xrefs" : [ "GOC:go_curators", "http://www.metacyc.org" ] + "xrefs" : [ "GOC:go_curators" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "primary metabolism" } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" @@ -13182,40 +12946,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071704", - "lbl" : "organic substance metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance metabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-03-08T03:32:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0071707", "lbl" : "immunoglobulin heavy chain V-D-J recombination", @@ -14181,62 +13911,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1902105", "lbl" : "regulation of leukocyte differentiation", @@ -14502,260 +14176,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], - "xrefs" : [ { - "val" : "IAO:0000233" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." - }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -15424,73 +14844,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -19427,6 +18780,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -19539,2856 +18916,6805 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "xrefs" : [ { - "val" : "RO:0000053" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" - }, - "xrefs" : [ { - "val" : "RO:0000056" + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "val" : "protein" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" - }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], + "xrefs" : [ { + "val" : "galen:Tube" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000055", + "lbl" : "vessel", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "A tubular structure that contains, conveys body fluid, such as blood or lymph.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000060", + "lbl" : "anatomical wall", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.", + "xrefs" : [ "FMA:82482" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "wall" + }, { + "pred" : "hasExactSynonym", + "val" : "wall of organ", + "xrefs" : [ "FMA:82482" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ wall", + "xrefs" : [ "FMA:82482" ] + } ], + "xrefs" : [ { + "val" : "FMA:82482" + }, { + "val" : "galen:Wall" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0009915" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001025", - "lbl" : "located in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000061", + "lbl" : "anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "CARO:0000003" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological structure" + }, { + "pred" : "hasExactSynonym", + "val" : "connected biological structure", + "xrefs" : [ "CARO:0000003" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010825" + }, { + "val" : "AEO:0000003" + }, { + "val" : "BILA:0000003" + }, { + "val" : "CARO:0000003" + }, { + "val" : "EHDAA2:0003003" + }, { + "val" : "EMAPA:0" + }, { + "val" : "FBbt:00007001" + }, { + "val" : "FMA:305751" + }, { + "val" : "FMA:67135" + }, { + "val" : "GAID:781" + }, { + "val" : "HAO:0000003" + }, { + "val" : "MA:0003000" + }, { + "val" : "MESH:D000825" + }, { + "val" : "SCTID:362889002" + }, { + "val" : "TAO:0000037" + }, { + "val" : "TGMA:0001823" + }, { + "val" : "VHOG:0001759" + }, { + "val" : "XAO:0003000" + }, { + "val" : "ZFA:0000037" + }, { + "val" : "http://dbpedia.org/ontology/AnatomicalStructure" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. 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Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." - }, + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." - }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "val" : "BilaDO:0000010" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" - }, + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" - }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000165", + "lbl" : "mouth", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "xrefs" : [ "Wikipedia:Mouth", "https://github.com/obophenotype/uberon/wiki/The-digestive-tract" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio oralis", + "xrefs" : [ "BTO:0004698", "FMA:49184", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "cavital oralis", + "xrefs" : [ "Wikipedia:Mouth" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavitas oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavum oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth cavity", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral region", + "xrefs" : [ "EHDAA2:0001326" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral vestibule", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "rima oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "stoma" + }, { + "pred" : "hasRelatedSynonym", + "val" : "stomatodaeum", + "xrefs" : [ "VHOG:0000812" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trophic apparatus", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibule of mouth", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibulum oris", + "xrefs" : [ "BTO:0001090" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010355" + }, { + "val" : "BTO:0001090" + }, { + "val" : "BTO:0004698" + }, { + "val" : "CALOHA:TS-1315" + }, { + "val" : "EFO:0000825" + }, { + "val" : "EHDAA2:0001326" + }, { + "val" : "EHDAA:542" + }, { + "val" : "EMAPA:16262" + }, { + "val" : "FBbt:00003126" + }, { + "val" : "FMA:49184" + }, { + "val" : "GAID:75" + }, { + "val" : "MA:0000341" + }, { + "val" : "MA:0002474" + }, { + "val" : "MAT:0000038" + }, { + "val" : "MESH:D009055" + }, { + "val" : "MIAA:0000038" + }, { + "val" : "SCTID:21082005" + }, { + "val" : "TADS:0000040" + }, { + "val" : "TAO:0000547" + }, { + "val" : "TAO:0000590" + }, { + "val" : "TGMA:0000131" + }, { + "val" : "VHOG:0000280" + }, { + "val" : "VHOG:0000812" + }, { + "val" : "Wikipedia:Mouth" + }, { + "val" : "XAO:0003029" + }, { + "val" : "ZFA:0000547" + }, { + "val" : "ZFA:0000590" + }, { + "val" : "galen:Mouth" + }, { + "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "val" : "https://github.com/obophenotype/uberon/issues/661" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "lbl" : "blood", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + "val" : "A fluid that is composed of blood plasma and erythrocytes.", + "xrefs" : [ "FMA:9670", "Wikipedia:Blood", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/9" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of blood" + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate blood" + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole blood", + "xrefs" : [ "BTO:0000089" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000046" + }, { + "val" : "BTO:0000089" + }, { + "val" : "CALOHA:TS-0079" + }, { + "val" : "EFO:0000296" + }, { + "val" : "EHDAA2:0000176" + }, { + "val" : "EHDAA:418" + }, { + "val" : "EMAPA:16332" + }, { + "val" : "ENVO:02000027" + }, { + "val" : "EV:0100047" + }, { + "val" : "FMA:9670" + }, { + "val" : "GAID:965" + }, { + "val" : "MA:0000059" + }, { + "val" : "MESH:D001769" + }, { + "val" : "MIAA:0000315" + }, { + "val" : "NCIT:C12434" + }, { + "val" : "TAO:0000007" + }, { + "val" : "UMLS:C0005767" + }, { + "val" : "VHOG:0000224" + }, { + "val" : "Wikipedia:Blood" + }, { + "val" : "XAO:0000124" + }, { + "val" : "ZFA:0000007" + }, { + "val" : "galen:Blood" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000179", + "lbl" : "haemolymphatic fluid", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." + "val" : "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blood or blood analog" + }, { + "pred" : "hasRelatedSynonym", + "val" : "circulating fluid" + } ], + "xrefs" : [ { + "val" : "CARO:0000081" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-04-08T04:38:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", + "lbl" : "blastula", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blastula embryo", + "xrefs" : [ "BILA:0000059" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastosphere", + "xrefs" : [ "Wikipedia:Blastula" ] + } ], "xrefs" : [ { - "val" : "RO:0002180" + "val" : "BILA:0000059" + }, { + "val" : "BTO:0000128" + }, { + "val" : "GAID:1294" + }, { + "val" : "MESH:D036703" + }, { + "val" : "OGEM:000006" + }, { + "val" : "Wikipedia:Blastula" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007011" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", + "lbl" : "musculature of body", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of develops from" + "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", + "xrefs" : [ "VSAO:0000033" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." - }, - "comments" : [ "TODO - add child relations from DOS" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - 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body continues after death stage" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002225", - "lbl" : "develops from part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002226", - "lbl" : "develops in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops_in y if x is located in y whilst x is developing" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", - "lbl" : "ends", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000475", + "lbl" : "organism subdivision", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of ends with" + "val" : "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.", + "xrefs" : [ "CARO:0000032", "CARO:DOS", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomic region", + "xrefs" : [ "MA:0002433" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "body part" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body region", + "xrefs" : [ "FMA:7153" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardinal body part", + "xrefs" : [ "FMA:7153" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010053" + }, { + "val" : "AEO:0000032" + }, { + "val" : "BILA:0000032" + }, { + "val" : "BIRNLEX:7" + }, { + "val" : "CALOHA:TS-2084" + }, { + "val" : "CARO:0000032" + }, { + "val" : "EFO:0000808" + }, { + "val" : "EHDAA2:0003032" + }, { + "val" : "EMAPA:36031" + }, { + "val" : "FBbt:00007009" + }, { + "val" : "FMA:7153" + }, { + "val" : "HAO:0000032" + }, { + "val" : "MA:0002433" + }, { + "val" : "MAT:0000293" + }, { + "val" : "MESH:D001829" + }, { + "val" : "MIAA:0000293" + }, { + "val" : "NCIT:C32221" + }, { + "val" : "TAO:0001308" + }, { + "val" : "TGMA:0001840" + }, { + "val" : "UMLS:C0229962" + }, { + "val" : "VHOG:0001758" + }, { + "val" : "Wikipedia:Body_part" + }, { + "val" : "XAO:0003013" + }, { + "val" : "ZFA:0001308" + }, { + "val" : "galen:BodyPart" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", - "lbl" : "ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000476", + "lbl" : "acellular anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "acellular anatomical structures", + "xrefs" : [ "ZFA:0000382" ] + } ], "xrefs" : [ { - "val" : "RO:0002230" + "val" : "AAO:0010268" + }, { + "val" : "AEO:0000040" + }, { + "val" : "BILA:0000040" + }, { + "val" : "CARO:0000040" + }, { + "val" : "EHDAA2:0003040" + }, { + "val" : "FBbt:00007013" + }, { + "val" : "FMA:63863" + }, { + "val" : "HAO:0000040" + }, { + "val" : "TAO:0000382" + }, { + "val" : "TGMA:0001841" + }, { + "val" : "XAO:0003162" + }, { + "val" : "ZFA:0000382" } ], "basicPropertyValues" : [ { - 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"subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002231" + "val" : "FBbt:00007277" + }, { + "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_start_location" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002232", - "lbl" : "has end location", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", + "lbl" : "tissue", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" + "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", + "xrefs" : [ "CARO:0000043" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "portion of tissue", + "xrefs" : [ "CARO:0000043" ] + }, { + "pred" : "hasExactSynonym", + "val" : "tissue portion" + }, { + "pred" : "hasNarrowSynonym", + "val" : "simple tissue", + "xrefs" : [ "AEO:0000043" ] + } ], "xrefs" : [ { - "val" : "RO:0002232" + "val" : "AAO:0000607" + }, { + "val" : "AAO:0010054" + }, { + "val" : "AEO:0000043" + }, { + "val" : "BILA:0000043" + }, { + "val" : "BIRNLEX:19" + }, { + "val" : "CALOHA:TS-2090" + }, { + "val" : "CARO:0000043" + }, { + "val" : "EHDAA2:0003043" + }, { + "val" : "EMAPA:35868" + }, { + "val" : "FBbt:00007003" + }, { + "val" : "FMA:9637" + }, { + "val" : "HAO:0000043" + }, { + "val" : "MA:0003002" + }, { + "val" : "MESH:D014024" + }, { + "val" : "NCIT:C12801" + }, { + "val" : "TAO:0001477" + }, { + "val" : "TGMA:0001844" + }, { + "val" : "UMLS:C0040300" + }, { + "val" : "VHOG:0001757" + }, { + "val" : "WBbt:0005729" + }, { + "val" : "XAO:0003040" + }, { + "val" : "ZFA:0001477" + }, { + "val" : "galen:Tissue" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "changed label and definition to reflect CARO2" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_end_location" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002233", - "lbl" : "has input", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000481", + "lbl" : "multi-tissue structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." + "val" : "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.", + "xrefs" : [ "CARO:0000055", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "multi-tissue structures", + "xrefs" : [ "ZFA:0001488" ] + } ], "xrefs" : [ { - "val" : "RO:0002233" + "val" : "AAO:0010048" + }, { + "val" : "AEO:0000055" + }, { + "val" : "BILA:0000055" + }, { + "val" : "CARO:0000055" + }, { + "val" : "EHDAA2:0003055" + }, { + "val" : "FBbt:00007010" + }, { + "val" : "HAO:0000055" + }, { + "val" : "TAO:0001488" + }, { + "val" : "TGMA:0001847" + }, { + "val" : "VHOG:0001762" + }, { + "val" : "XAO:0003037" + }, { + "val" : "ZFA:0001488" } ], "basicPropertyValues" : [ { - 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"plasma", + "xrefs" : [ "MA:0002501" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "portion of plasma", + "xrefs" : [ "FMA:62970" ] + }, { + "pred" : "hasExactSynonym", + "val" : "blood plasm" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of blood plasma" + } ], + "xrefs" : [ { + "val" : "BTO:0000131" + }, { + "val" : "CALOHA:TS-0800" + }, { + "val" : "EFO:0001905" + }, { + "val" : "EMAPA:35690" + }, { + "val" : "FMA:62970" + }, { + "val" : "GAID:1178" + }, { + "val" : "MA:0002501" + }, { + "val" : "MAT:0000052" + }, { + "val" : "MESH:D010949" + }, { + "val" : "MIAA:0000052" + }, { + "val" : "NCIT:C13356" + }, { + "val" : "UMLS:C0032105" + }, { + "val" : "Wikipedia:Blood_plasma" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "lbl" : "blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vessel through which blood circulates in the body.", + "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "vascular element", + "xrefs" : [ "EMAPA:35993" ] + }, { + "pred" : "hasExactSynonym", + "val" : "region of vascular tree organ", + "xrefs" : [ "FMA:50722" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vascular tree organ region", + "xrefs" : [ "FMA:50722" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "vas sanguineum", + "xrefs" : [ "Wikipedia:Blood_vessel" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011004" + }, { + "val" : 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Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].", + "xrefs" : [ "FMA:63916", "MESH:A10.272.491", "https://github.com/obophenotype/uberon/issues/225" ] + }, + "comments" : [ "The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "BTO:0000393" + }, { + "val" : "CALOHA:TS-0278" + }, { + "val" : "EFO:0002548" + }, { + "val" : "FMA:63916" + }, { + "val" : "GAID:520" + }, { + "val" : "MESH:D004727" + }, { + "val" : "NCIT:C12481" + }, { + "val" : "SCTID:27168002" + }, { + "val" : "UMLS:C0014257" + }, { + "val" : "galen:Endothelium" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002049", + "lbl" : "vasculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.", + "xrefs" : [ "ZFA:0005249" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "vascular network", + "xrefs" : [ "FMA:69050" ] + } ], + "xrefs" : [ { + "val" : "BTO:0003718" + }, { + "val" : "FMA:69050" + }, { + "val" : "TAO:0005249" + }, { + "val" : "ZFA:0005249" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "see also: vascular system. Consider merging?" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002050", + "lbl" : "embryonic structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical structure that is part of an embryo.", + "xrefs" : [ "BTO:0000174", "ZFIN:curator" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "developing embryonic structure", + "xrefs" : [ "FBbt:00004208" ] + }, { + "pred" : "hasExactSynonym", + "val" : "embryonic anatomical structure", + "xrefs" : [ "RETIRED_EHDAA2:0003169" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "developing structure" + }, { + "pred" : "hasRelatedSynonym", + "val" : "embryonale Struktur", + "xrefs" : [ "BTO:0000174" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "embryonic structures", + "xrefs" : [ "ZFA:0001105" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000138" + }, { + "val" : "BILA:0000034" + }, { + "val" : "BTO:0000174" + }, { + "val" : "CALOHA:TS-2110" + }, { + "val" : "EFO:0000461" + }, { + "val" : "FBbt:00004208" + }, { + "val" : "FMA:69067" + }, { + "val" : "GAID:407" + }, { + "val" : "MESH:D004628" + }, { + "val" : "NCIT:C13229" + }, { + "val" : "RETIRED_EHDAA2:0003169" + }, { + "val" : "SCTID:667009" + }, { + "val" : "TAO:0001105" + }, { + "val" : "UMLS:C0013948" + }, { + "val" : "VSAO:0000178" + }, { + "val" : "XAO:0003042" + }, { + "val" : "ZFA:0001105" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002075", + "lbl" : "viscus", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.", + "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "visceral organ", + "xrefs" : [ "RETIRED_EHDAA2:0002201" ] + }, { + "pred" : "hasExactSynonym", + "val" : "visceral organ system", + "xrefs" : [ "MA:0000019" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "splanchnic tissue", + "xrefs" : [ "BTO:0001491" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "viscera" + }, { + "pred" : "hasRelatedSynonym", + "val" : "visceral tissue", + "xrefs" : [ "BTO:0001491" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010386" + }, { + "val" : "BTO:0001491" + }, { + "val" : "EHDAA:512" + }, { + "val" : "EMAPA:16245" + }, { + "val" : "FMA:7085" + }, { + "val" : "MA:0000019" + }, { + "val" : "MESH:D014781" + }, { + "val" : "NCIT:C28287" + }, { + "val" : "RETIRED_EHDAA2:0002201" + }, { + "val" : "SCTID:118760003" + }, { + "val" : "UMLS:C0042779" + }, { + "val" : "Wikipedia:Viscus" + }, { + "val" : "XAO:0003034" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", + "lbl" : "postcranial axial skeleton", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", + "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] + }, + "comments" : [ "previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "axial skeleton", + "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] + }, { + "pred" : "hasExactSynonym", + "val" : "post-cranial axial skeleton" + } ], + "xrefs" : [ { + "val" : "AAO:0000034" + }, { + "val" : "EFO:0000942" + }, { + "val" : "EHDAA2:0000161" + }, { + "val" : "EHDAA:5049" + }, { + "val" : "EMAPA:37721" + }, { + "val" : "FMA:71221" + }, { + "val" : "MA:0002986" + }, { + "val" : "MAT:0000148" + }, { + "val" : "MIAA:0000148" + }, { + "val" : "TAO:0000317" + }, { + "val" : "VHOG:0000317" + }, { + "val" : "VSAO:0000093" + }, { + "val" : "XAO:0003073" + }, { + "val" : "ZFA:0000317" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", + "lbl" : "trunk", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.", + "xrefs" : [ "TAO:0001115", "UBERONREF:0000006", "Wikipedia:Torso" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "thoracolumbar region" + }, { + "pred" : "hasExactSynonym", + "val" : "torso" + }, { + "pred" : "hasExactSynonym", + "val" : "trunk region", + "xrefs" : [ "XAO:0000054" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Rumpf", + "xrefs" : [ "BTO:0001493" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010339" + }, { + "val" : "BILA:0000116" + }, { + "val" : "BTO:0001493" + }, { + "val" : "CALOHA:TS-1071" + }, { + "val" : "EFO:0000966" + }, { + "val" : "EMAPA:31857" + }, { + "val" : "FMA:7181" + }, { + "val" : "MA:0000004" + }, { + "val" : "MAT:0000296" + }, { + "val" : 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From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].", + "xrefs" : [ "Wikipedia:Sclerotome", "XB:curator", "https://github.com/obophenotype/uberon/issues/316" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "sclerotomes", + "xrefs" : [ "TAO:0001080" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "sclerotomus", + "xrefs" : [ "Wikipedia:Sclerotome" ] + } ], "xrefs" : [ { - "val" : "RO:0002427" + "val" : "AAO:0010571" + }, { + "val" : "AEO:0000212" + }, { + "val" : "EHDAA2:0003439" + }, { + "val" : "EMAPA:31159" + }, { + "val" : "FMA:295652" + }, { + "val" : "NCIT:C34287" + }, { + "val" : "TAO:0001080" + }, { + "val" : "UMLS:C0183176" + }, { + "val" : "VHOG:0000680" + }, { + "val" : "Wikipedia:Sclerotome" + }, { + "val" : "XAO:0000397" + }, { + "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_downstream_of_or_within" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", - "lbl" : "involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", - "lbl" : "involved in or involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", - "lbl" : "contributes to morphology of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. 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Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", - "lbl" : "composed primarily of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", - "lbl" : "has part that occurs in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", + "lbl" : "compound organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", + "xrefs" : [ "CARO:0000024" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "lbl" : "receives input from", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "lbl" : "sends output to", - "type" : "PROPERTY", - "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "organ" + } ], + "xrefs" : [ { + "val" : "AAO:0010015" + }, { + "val" : "AEO:0000024" + }, { + "val" : "BILA:0000024" + }, { + "val" : "CARO:0000024" + }, { + "val" : "EHDAA2:0003024" + }, { + "val" : "HAO:0000024" + }, { + "val" : "TADS:0000598" + }, { + "val" : "TAO:0000496" + }, { + "val" : "TGMA:0001837" + }, { + "val" : "VHOG:0001723" + }, { + "val" : "XAO:0003041" + }, { + "val" : "ZFA:0000496" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", - "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", - "lbl" : "existence starts during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002489", - "lbl" : "existence starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002490", - "lbl" : "existence overlaps", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002491", - "lbl" : "existence starts and ends during", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", + "lbl" : "mesenchyme", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.", + "xrefs" : [ "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up", "https://en.wikipedia.org/wiki/Mesenchyme", "https://github.com/obophenotype/uberon/issues/1641" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "exists during" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", - "lbl" : "existence ends during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002493", - "lbl" : "existence ends with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", - "lbl" : "transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002495", - "lbl" : "immediate transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002496", - "lbl" : "existence starts during or after", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", - "lbl" : "existence ends during or before", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002500", - "lbl" : "causal agent in process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002501", - "lbl" : "causal relation between processes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002502", - "lbl" : "depends on", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/BFO_0000169" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002551", - "lbl" : "has skeleton", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002565", - "lbl" : "results in movement of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "val" : "mesenchymal tissue" + }, { + "pred" : "hasExactSynonym", + "val" : "mesenchyme tissue" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of mesenchymal tissue" + }, { + "pred" : "hasExactSynonym", + "val" : "portion of mesenchyme tissue" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "mesenchyma", + "xrefs" : [ "Wikipedia:Mesenchyme" ] + } ], "xrefs" : [ { - "val" : "RO:0002565" + "val" : "AAO:0010427" + }, { + "val" : "AEO:0000145" + }, { + "val" : "BTO:0001393" + }, { + "val" : "CALOHA:TS-0620" + }, { + "val" : "EHDAA2:0003145" + }, { + "val" : "EV:0100007" + }, { + "val" : "NCIT:C13301" + }, { + "val" : "TAO:0000393" + }, { + "val" : "UMLS:C0162415" + }, { + "val" : "VHOG:0000170" + }, { + "val" : "Wikipedia:Mesenchyme" + }, { + "val" : "XAO:0003046" + }, { + "val" : "ZFA:0000393" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_movement_of" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002567", - "lbl" : "biomechanically related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002568", - "lbl" : "has muscle antagonist", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002569", - "lbl" : "has branching part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of branching part of" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002570", - "lbl" : "conduit for", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", + "lbl" : "future coelemic cavity lumen", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." + "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "future coelomic cavity lumen" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body cavity precursor" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002571", - "lbl" : "lumen of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", + "lbl" : "intraembryonic coelom", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." + "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", + "xrefs" : [ "MGI:anna", "MP:0012187" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "somatic coelom", + "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] + } ], + "xrefs" : [ { + "val" : "EHDAA:251" + }, { + "val" : "EMAPA:16088" + }, { + "val" : "NCIT:C34195" + }, { + "val" : "UMLS:C1512940" + }, { + "val" : "VHOG:0000316" + }, { + "val" : "Wikipedia:Intraembryonic_coelom" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002572", - "lbl" : "luminal space of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", + "lbl" : "epithelial tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" + "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", + "xrefs" : [ "GO:0060562", "PMID:12526790" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "epithelial or endothelial tube" + } ], + "xrefs" : [ { + "val" : "AEO:0000114" + }, { + "val" : "EHDAA2:0003114" + }, { + "val" : "FBbt:00007474" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - 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} - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002588", - "lbl" : "results in assembly of", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "foramen", + "xrefs" : [ "EHDAA2:0003080" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasNarrowSynonym", + "val" : "foramina", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "opening" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "ostia" + }, { + "pred" : "hasRelatedSynonym", + "val" : "ostium" + } ], "xrefs" : [ { - "val" : "RO:0002588" + "val" : "AEO:0000080" + }, { + "val" : "EHDAA2:0003080" + }, { + "val" : "FMA:242873" + }, { + "val" : "SCTID:346902003" + }, { + "val" : "Wikipedia:Foramen" } ], "basicPropertyValues" : [ { - 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Editors notes: TODO - develops_from" ], "xrefs" : [ { - "val" : "RO:0012003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "val" : "EMAPA:37744" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-06-08T17:21:33Z" + "val" : "MA:0003047" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "SCTID:309311006" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "acts_on_population_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012004", - "lbl" : "is small molecule regulator of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "val" : "VSAO:0000015" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-06-24T13:15:17Z" + "val" : "XAO:0004038" + }, { + "val" : "ZFA:0005619" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012005", - "lbl" : "is small molecule activator of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", + "lbl" : "skeletal element", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is a small molecule that activates the process" + "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "AAO:0011129" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-06-24T13:15:26Z" + "val" : "TAO:0001890" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Is_small_molecule_activator_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0012008", - "lbl" : "results in fusion of", - "type" : "PROPERTY", - "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0012008" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0003-1813-6857" + "val" : "VSAO:0000128" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2021-02-26T07:28:29Z" + "val" : "XAO:0004012" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "ZFA:0005494" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fusion_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013001", - "lbl" : "has synaptic IO in region", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "has synaptic input or output in" + "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-17T09:26:52Z" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0013007", - "lbl" : "has sensory dendrite in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", + "lbl" : "articular system", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." + "val" : "Anatomical system that consists of all the joints of the body.", + "xrefs" : [ "VSAO:0000181" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has sensory dendrite location" + "val" : "joint system", + "xrefs" : [ "FMA:23878" ] }, { "pred" : "hasExactSynonym", - "val" : "has sensory terminal in" + "val" : "set of all joints of body", + "xrefs" : [ "FMA:23878" ] }, { - "pred" : "hasExactSynonym", - "val" : "has sensory terminal location" + "pred" : "hasRelatedSynonym", + "val" : "set of all joints" + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of joints of body", + "xrefs" : [ "FMA:23878" ] } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "https://orcid.org/0000-0002-1373-1705" + "xrefs" : [ { + "val" : "EMAPA:35150" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2020-07-20T12:10:09Z" + "val" : "FMA:23878" + }, { + "val" : "MA:0003007" + }, { + "val" : "SCTID:361827000" + }, { + "val" : "VSAO:0000181" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015006", - "lbl" : "different in magnitude relative to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). 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Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015010", - "lbl" : "has relative magnitude", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0015011", - "lbl" : "has cross section", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", + "lbl" : "cardiovascular system endothelium", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "val" : "An endothelium that is part of the cardiovascular system.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - 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Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blastula embryo", - "xrefs" : [ "BILA:0000059" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastosphere", - "xrefs" : [ "Wikipedia:Blastula" ] - } ], + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "BILA:0000059" + "val" : "BILA:0000010" }, { - "val" : "BTO:0000128" + "val" : "CARO:0001002" }, { - "val" : "GAID:1294" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "MESH:D036703" + "val" : "FMA:24137" }, { - "val" : "OGEM:000006" + "val" : "NCIT:C34022" }, { - "val" : "Wikipedia:Blastula" + "val" : "UMLS:C1515977" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check relationship with epiblast. 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See https://github.com/obophenotype/uberon/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "val" : "consider FBbt:00005541 ! cardiogenic mesoderm" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "review EHDAA2 placement" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", + "lbl" : "cleaving embryo", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Organism at the cleavage stage.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "BILA:0000058" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", + "lbl" : "presumptive gut", + "type" : "CLASS", + "meta" : { "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "body fluid or substance", - "xrefs" : [ "MA:0002450" ] - }, { - "pred" : "hasExactSynonym", - "val" : "body substance", - "xrefs" : [ "FMA:9669" ] + "val" : "future digestive tract" }, { "pred" : "hasExactSynonym", - "val" : "organism substance", - "xrefs" : [ "CARO:0000004" ] + "val" : "future digestive tube" }, { "pred" : "hasExactSynonym", - 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In vertebrates, this is based on the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "simple epithelium", - "xrefs" : [ "FMA:45561" ] + "val" : "axial subdivision of organism" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "unilaminar epithelia", - "xrefs" : [ "ZFA:0001495" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010062" - }, { - "val" : "AEO:0000073" - }, { - "val" : "BILA:0000073" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000073" - }, { - "val" : "EHDAA2:0003073" - }, { - "val" : "FMA:45561" - }, { - "val" : "HAO:0000073" - }, { - "val" : "NCIT:C33554" - }, { - "val" : "SCTID:309043004" - }, { - "val" : "TAO:0001495" - }, { - "val" : "UMLS:C0682574" - }, { - "val" : "XAO:0004007" + "val" : "body segment" }, { - "val" : "ZFA:0001495" + "pred" : "hasRelatedSynonym", + "val" : "main body segment" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" + "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000915", - "lbl" : "thoracic segment of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", + "lbl" : "embryonic cardiovascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Subdivision of trunk that lies between the head and the abdomen.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A cardiovascular system that is part of a conceptus.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "thorax", - "xrefs" : [ "MA:0000022" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "anterior subdivision of trunk" + "val" : "conceptus cardiovascular system" }, { "pred" : "hasRelatedSynonym", - "val" : "upper body" + "val" : "embryonic circulatory system" }, { "pred" : "hasRelatedSynonym", - "val" : "upper trunk", - "xrefs" : [ "FMA:259209" ] + "val" : "fetal circulatory system" } ], "xrefs" : [ { - "val" : "EMAPA:35862" - }, { - "val" : "FMA:259209" - }, { - "val" : "MA:0000022" + "val" : "EHDAA2:0000216" }, { - "val" : "SCTID:302551006" + "val" : "FMA:305965" }, { - "val" : "Wikipedia:Thorax" + "val" : "NCIT:C34148" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24613,155 +27467,110 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000922", - "lbl" : "embryo", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", + "lbl" : "coelom", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", - "xrefs" : [ "BTO:0000379", "FB:FBrf0039741", "FB:FBrf0041814", "GO:0009790", "Wikipedia:Embryo" ] + "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic organism", - "xrefs" : [ "BILA:0000056" ] + "pred" : "hasNarrowSynonym", + "val" : "enterocoelom", + "xrefs" : [ "NCBITaxon:33511" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "haemocoelom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "schizocoelom" }, { "pred" : "hasRelatedSynonym", - "val" : "developing organism", - "xrefs" : [ "BILA:0000056" ] + "val" : "coelem" }, { "pred" : "hasRelatedSynonym", - "val" : "developmental tissue" + "val" : "coelomic cavity", + "xrefs" : [ "EHDAA2:0004731" ] } ], "xrefs" : [ { - "val" : "AAO:0011035" - }, { - "val" : "AEO:0000169" - }, { - "val" : "BILA:0000056" - }, { - "val" : "BSA:0000039" - }, { - "val" : "BTO:0000379" - }, { - "val" : "CALOHA:TS-0229" - }, { - "val" : "EFO:0001367" - }, { - "val" : "EHDAA2:0000002" - }, { - "val" : "EHDAA2_RETIRED:0003236" - }, { - "val" : "EHDAA:38" - }, { - "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" - }, { - "val" : "FMA:69068" - }, { - "val" : "GAID:963" - }, { - "val" : "MAT:0000226" - }, { - "val" : "MESH:D004622" - }, { - "val" : "MIAA:0000019" - }, { - "val" : "NCIT:C28147" - }, { - "val" : "OGEM:000001" - }, { - "val" : "SCTID:57991002" - }, { - "val" : "UMLS:C0013935" - }, { - "val" : "VHOG:0001766" + "val" : "EHDAA2:0004731" }, { - "val" : "Wikipedia:Embryo" + "val" : "Wikipedia:Coelom" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." }, { - "val" : "XAO:0000113" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { - "val" : "ZFA:0000103" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", + "lbl" : "meso-epithelium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesoderm-derived epithelium" }, { - "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" + "pred" : "hasExactSynonym", + "val" : "mesoepithelium" + } ], + "xrefs" : [ { + "val" : "FMA:86452" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/503" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "lbl" : "germ layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012429", + "lbl" : "hematopoietic tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.", - "xrefs" : [ "Wikipedia:Germ_layer", "https://github.com/obophenotype/uberon/issues/203" ] + "val" : "Blood-forming tissue, consisting of reticular fibers and cells.", + "xrefs" : [ "http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue" ] }, - "comments" : [ "Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "embryonic tissue", - "xrefs" : [ "FMA:69069" ] + "pred" : "hasExactSynonym", + "val" : "haemopoietic tissue", + "xrefs" : [ "FMA:14073" ] }, { "pred" : "hasExactSynonym", - "val" : "germinal layer", - "xrefs" : [ "ncithesaurus:Germinal_Layer" ] + "val" : "hematopoietic tissue", + "xrefs" : [ "FMA:14073" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "primary germ layer", - "xrefs" : [ "GO:0001704", "ZFA:0001122" ] + "pred" : "hasExactSynonym", + "val" : "hemopoietic tissue", + "xrefs" : [ "FMA:14073" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layer" + "pred" : "hasExactSynonym", + "val" : "textus haemopoieticus", + "xrefs" : [ "FMA:14073" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layers" + "pred" : "hasNarrowSynonym", + "val" : "bone marrow tissue", + "xrefs" : [ "NCBITaxon:9606" ] } ], "xrefs" : [ { - "val" : "AAO:0000480" - }, { - "val" : "BILA:0000035" - }, { - "val" : "BTO:0000556" - }, { - "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" - }, { - "val" : "FMA:69069" - }, { - "val" : "GAID:1303" - }, { - "val" : "MESH:D005855" - }, { - "val" : "NCIT:C12950" - }, { - "val" : "NCIT:C54105" - }, { - "val" : "TAO:0001122" - }, { - "val" : "UMLS:C0920502" - }, { - "val" : "UMLS:C1708239" - }, { - "val" : "VHOG:0001223" + "val" : "CALOHA:TS-2142" }, { - "val" : "Wikipedia:Germ_layer" + "val" : "FMA:14073" }, { - "val" : "XAO:0003011" + "val" : "NCIT:C13051" }, { - "val" : "ZFA:0001122" + "val" : "UMLS:C0229619" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24769,483 +27578,250 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", - "lbl" : "ectoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", + "lbl" : "subdivision of tube", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013686", + "lbl" : "anatomical conduit space", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", - "xrefs" : [ "Wikipedia:Ectoderm" ] + "val" : "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].", + "xrefs" : [ "FMA:9338", "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic ectoderm", - "xrefs" : [ "VHOG:0000153" ] + "pred" : "hasNarrowSynonym", + "val" : "foramen space" } ], "xrefs" : [ { - "val" : "AAO:0000137" - }, { - "val" : "BILA:0000036" - }, { - "val" : "BTO:0000315" - }, { - "val" : "CALOHA:TS-0216" - }, { - "val" : "EFO:0000414" - }, { - "val" : "EHDAA2:0000428" - }, { - "val" : "EMAPA:16069" - }, { - "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" - }, { - "val" : "FMA:69070" - }, { - "val" : "GAID:1304" - }, { - "val" : "MAT:0000155" - }, { - "val" : "MAT:0000173" - }, { - "val" : "MESH:D004475" - }, { - "val" : "MIAA:0000173" - }, { - "val" : "NCIT:C12703" - }, { - "val" : "SCTID:362851007" - }, { - "val" : "TAO:0000016" - }, { - "val" : "UMLS:C0013574" - }, { - "val" : "VHOG:0000153" + "val" : "FMA:9338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "Wikipedia:Ectoderm" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "XAO:0000001" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "ZFA:0000016" - } ], + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", + "lbl" : "main body axis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - 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In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", - "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] + "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", + "xrefs" : [ "CARO:0020001" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neurological system", - "xrefs" : [ "GO:0050877" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "nerve net", - "xrefs" : [ "Wikipedia:Nerve_net" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "systema nervosum", - "xrefs" : [ "Wikipedia:Nervous_system" ] + "val" : "anatomical cluster", + "xrefs" : [ "CARO:0020001" ] } ], "xrefs" : [ { - "val" : "AAO:0000324" - }, { - "val" : "BILA:0000079" - }, { - "val" : "BIRNLEX:844" - }, { - "val" : "BTO:0001484" - }, { - "val" : "CALOHA:TS-1313" - }, { - "val" : "EFO:0000802" - }, { - "val" : "EHDAA2:0001246" - }, { - "val" : "EHDAA:826" - }, { - "val" : "EMAPA:16469" - }, { - "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" - }, { - "val" : "FMA:7157" - }, { - "val" : "GAID:466" - }, { - "val" : "MA:0000016" - }, { - "val" : "MAT:0000026" - }, { - "val" : "MESH:D009420" - }, { - "val" : "MIAA:0000026" - }, { - "val" : "NCIT:C12755" - }, { - "val" : "SCTID:278196006" - }, { - "val" : "TAO:0000396" - }, { - "val" : "UMLS:C0027763" - }, { - "val" : "VHOG:0000402" - }, { - "val" : "WBbt:0005735" + "val" : "CARO:0020001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "Wikipedia:Nervous_system" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "XAO:0000177" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "ZFA:0000396" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", + "lbl" : "disconnected anatomical group", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", + "xrefs" : [ "CARO:0020000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "xrefs" : [ { + "val" : "CARO:0020000" }, { - "val" : "neuronames:3236" + "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", + "lbl" : "anatomical collection", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "lbl" : "central nervous system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", + "lbl" : "future mouth", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. 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See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "GAID:570" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "val" : "MA:0000167" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "MAT:0000457" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "MESH:D002490" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "NCIT:C12438" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "val" : "SCTID:278199004" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "val" : "TAO:0000012" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" }, { - "val" : "UMLS:C0927232" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { - "val" : "VHOG:0000293" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "Wikipedia:Central_nervous_system" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "val" : "XAO:0000215" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "ZFA:0000012" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "neuronames:854" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001048", - "lbl" : "primordium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].", - "xrefs" : [ "BTO:0001886", "FB:DJS", "FB:FBrf0089570", "http://flybase.org/reports/FBrf0178740.html" ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "bud" - }, { - "pred" : "hasRelatedSynonym", - "val" : "future organ" + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "hasRelatedSynonym", - "val" : "placode", - "xrefs" : [ "FBbt:00005495" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000066" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "primordia", - "xrefs" : [ "XAO:0003043" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" }, { - "pred" : "hasRelatedSynonym", - "val" : "rudiment" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "xrefs" : [ { - "val" : "AEO:0000171" - }, { - "val" : "BTO:0001886" + "val" : "GOREL:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "EFO:0001652" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "xrefs" : [ { + "val" : "GOREL:0002004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "EHDAA2:0003171" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { - "val" : "FBbt:00005495" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "FMA:86589" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "MAT:0000482" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { - "val" : "NCIT:C34275" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "UMLS:C0678727" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "val" : "Wikipedia:Primordium" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "XAO:0003043" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001049", - "lbl" : "neural tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].", - "xrefs" : [ "Wikipedia:Neural_tube" ] + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural primordium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tubus neuralis", - "xrefs" : [ "Wikipedia:Neural_tube" ] - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0010617" - }, { - "val" : "BTO:0001057" - }, { - "val" : "CALOHA:TS-2371" - }, { - "val" : "DHBA:10154" - }, { - "val" : "EHDAA2:0001254" - }, { - "val" : "EHDAA:2869" - }, { - "val" : "EHDAA:908" - }, { - "val" : "EMAPA:16164" - }, { - "val" : "EMAPA:16757" - }, { - "val" : "FMA:293882" - }, { - "val" : "MAT:0000069" - }, { - "val" : "MIAA:0000069" - }, { - "val" : "NCIT:C34226" - }, { - "val" : "SCTID:362852000" - }, { - "val" : "TAO:0001135" - }, { - "val" : "UMLS:C0231024" - }, { - "val" : "VHOG:0000307" - }, { - "val" : "Wikipedia:Neural_tube" - }, { - "val" : "XAO:0003204" - }, { - "val" : "ZFA:0001135" - }, { - "val" : "neuronames:1365" + "val" : "RO:0002007" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", - "lbl" : "anatomical entity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", - "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. 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Consider merging?" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002050", - "lbl" : "embryonic structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that is part of an embryo.", - "xrefs" : [ "BTO:0000174", "ZFIN:curator" ] + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "developing embryonic structure", - "xrefs" : [ "FBbt:00004208" ] - }, { - "pred" : "hasExactSynonym", - "val" : "embryonic anatomical structure", - "xrefs" : [ "RETIRED_EHDAA2:0003169" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonale Struktur", - "xrefs" : [ "BTO:0000174" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "embryonic structures", - "xrefs" : [ "ZFA:0001105" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000138" - }, { - "val" : "BILA:0000034" - }, { - "val" : "BTO:0000174" - }, { - "val" : "CALOHA:TS-2110" - }, { - "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" - }, { - "val" : "FMA:69067" - }, { - "val" : "GAID:407" - }, { - "val" : "MESH:D004628" - }, { - "val" : "NCIT:C13229" - }, { - "val" : "RETIRED_EHDAA2:0003169" - }, { - "val" : "SCTID:667009" - }, { - "val" : "TAO:0001105" - }, { - "val" : "UMLS:C0013948" - }, { - "val" : "VSAO:0000178" - }, { - "val" : "XAO:0003042" - }, { - "val" : "ZFA:0001105" - } ], + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002075", - "lbl" : "viscus", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.", - "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral organ", - "xrefs" : [ "RETIRED_EHDAA2:0002201" ] - }, { - "pred" : "hasExactSynonym", - "val" : "visceral organ system", - "xrefs" : [ "MA:0000019" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic tissue", - "xrefs" : [ "BTO:0001491" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "viscera" - }, { - "pred" : "hasRelatedSynonym", - "val" : "visceral tissue", - "xrefs" : [ "BTO:0001491" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010386" - }, { - "val" : "BTO:0001491" - }, { - "val" : "EHDAA:512" - }, { - "val" : "EMAPA:16245" - }, { - "val" : "FMA:7085" - }, { - "val" : "MA:0000019" - }, { - "val" : "MESH:D014781" - }, { - "val" : "NCIT:C28287" - }, { - "val" : "RETIRED_EHDAA2:0002201" - }, { - "val" : "SCTID:118760003" - }, { - "val" : "UMLS:C0042779" - }, { - "val" : "Wikipedia:Viscus" - }, { - "val" : "XAO:0003034" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", - "lbl" : "postcranial axial skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", - "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, - "comments" : [ "previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "axial skeleton", - "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] - }, { - "pred" : "hasExactSynonym", - "val" : "post-cranial axial skeleton" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0000034" - }, { - "val" : "EFO:0000942" - }, { - "val" : "EHDAA2:0000161" - }, { - "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:37721" - }, { - "val" : "FMA:71221" - }, { - "val" : "MA:0002986" - }, { - "val" : "MAT:0000148" - }, { - "val" : "MIAA:0000148" - }, { - "val" : "TAO:0000317" - }, { - "val" : "VHOG:0000317" - }, { - "val" : "VSAO:0000093" - }, { - "val" : "XAO:0003073" - }, { - "val" : "ZFA:0000317" + "val" : "RO:0002131" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "overlaps" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", - "lbl" : "trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.", - "xrefs" : [ "TAO:0001115", "UBERONREF:0000006", "Wikipedia:Torso" ] + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracolumbar region" - 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"id" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "lbl" : "hemolymphoid system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hematolymphoid system" - }, { - "pred" : "hasExactSynonym", - "val" : "lymphomyeloid complex" - }, { - "pred" : "hasRelatedSynonym", - "val" : "haemolymphoid system" - } ], - "xrefs" : [ { - "val" : "CALOHA:TS-2018" - }, { - "val" : "EHDAA2:0004615" - }, { - "val" : "EMAPA:18765" - }, { - "val" : "FMA:74562" - }, { - "val" : "MA:0000013" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002204", - "lbl" : "musculoskeletal system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of the muscular and skeletal systems.", - "xrefs" : [ "VSAO:0000031", "VSAO:curator", "https://github.com/obophenotype/uberon/issues/77" ] + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "musculo-skeletal system" - } ], - "xrefs" : [ { - "val" : "AAO:0010546" - }, { - "val" : "CALOHA:TS-1311" - 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e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" }, { - "val" : "XAO:0000168" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + }, + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - 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"val" : "chest cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "pectoral cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "space of thoracic compartment", - "xrefs" : [ "FMA:7565" ] - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic lumen" - } ], - "xrefs" : [ { - "val" : "EMAPA:36497" - }, { - "val" : "FMA:7565" - }, { - "val" : "GAID:93" - }, { - "val" : "MA:0000032" - }, { - "val" : "MESH:D035423" - }, { - "val" : "NCIT:C12905" - }, { - "val" : "SCTID:243949006" - }, { - "val" : "UMLS:C0230139" - }, { - "val" : "Wikipedia:Thoracic_cavity" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", - "lbl" : "coelemic cavity lumen", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.", - "xrefs" : [ "BTO:0001707" ] + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "comments" : [ "EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "body cavity", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity", - "xrefs" : [ "EHDAA2:0000267" ] - }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity lumen", - "xrefs" : [ "EHDAA2:0000267" ] - }, { - "pred" : "hasExactSynonym", - "val" : "main body cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "space of body compartment", - "xrefs" : [ "FMA:85006" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "ventral body cavity", - "xrefs" : [ "NCBITaxon:7742" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "celom", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "coelom" - }, { - "pred" : "hasRelatedSynonym", - "val" : "coelome", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "hemocoel", - "xrefs" : [ "FBbt:00005060" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000186" - }, { - "val" : "BTO:0001707" - }, { - "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" - }, { - "val" : "FMA:85006" - }, { - "val" : "NCIT:C25444" - }, { - "val" : "RETIRED_EHDAA2:0003186" - }, { - "val" : "SCTID:361348008" - }, { - "val" : "TAO:0001438" - }, { - "val" : "UMLS:C0333343" - }, { - "val" : "ZFA:0001438" - }, { - "val" : "galen:BodyCavity" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "lbl" : "notochord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A flexible rod-shaped body found in embryos of all chordates. 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In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic notocord" - }, { - "pred" : "hasExactSynonym", - "val" : "notocord", - "xrefs" : [ "ZFA:0000135" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "notochorda", - "xrefs" : [ "Wikipedia:Notochord" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000327" - }, { - "val" : "BTO:0001768" - }, { - "val" : "CALOHA:TS-0690" - }, { - "val" : "EHDAA2:0001277" - }, { - "val" : "EHDAA:1241" - }, { - "val" : "EHDAA:6021" - }, { - "val" : "EMAPA:16191" - }, { - "val" : "EV:0100002" - }, { - "val" : "FMA:85521" - }, { - "val" : "GAID:1311" - }, { - "val" : "MAT:0000281" - }, { - "val" : "MESH:D009672" - }, { - "val" : "NCIT:C12463" - }, { - "val" : "SCTID:308820002" - }, { - "val" : "TAO:0000135" - }, { - "val" : "UMLS:C0028439" - }, { - "val" : "VHOG:0000199" - }, { - "val" : "VSAO:0000032" - }, { - "val" : "Wikipedia:Notochord" - }, { - "val" : "XAO:0000055" - }, { - "val" : "ZFA:0000135" - }, { - "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "lbl" : "somite", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.", - "xrefs" : [ "DOI:10.1111/j.1439-0426.2012.01987.x", "Wikipedia:Somite" ] + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "comments" : [ "When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. 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For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0010578" - }, { - "val" : "BTO:0001764" - }, { - "val" : "CALOHA:TS-0676" - }, { - "val" : "EHDAA2:0004419" - }, { - "val" : "EMAPA:32737" - }, { - "val" : "FMA:86666" - }, { - "val" : "GAID:1310" - }, { - "val" : "MAT:0000066" - }, { - "val" : "MESH:D009432" - }, { - "val" : "MIAA:0000066" - }, { - "val" : "NCIT:C34222" - }, { - "val" : "SCTID:361462002" - }, { - "val" : "UMLS:C0027789" - }, { - "val" : "VHOG:0000057" - }, { - "val" : "Wikipedia:Neural_crest" - }, { - "val" : "XAO:0000048" - }, { - "val" : "ZFA:0000045" - }, { - "val" : "neuronames:1366" + "val" : "RO:0002180" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002346", - "lbl" : "neurectoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Embryonic ectoderm that gives rise to nervous tissue.", - "xrefs" : [ "Wikipedia:Neuroectoderm" ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "This is the transitive form of the develops from relation" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neural ectoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "neuroectoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epithelium tubi neuralis; 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See also: Leydig and epigonal organs" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider placement of NCIT:C53466 medullary bone" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "lbl" : "connective tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue", - "xrefs" : [ "FMA:9640" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bindegewebe", - "xrefs" : [ "BTO:0000421" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0000098" - }, { - "val" : "BTO:0000421" - }, { - "val" : "CALOHA:TS-2009" - }, { - "val" : "EFO:0000952" - }, { - "val" : "EMAPA:35251" - }, { - "val" : "FMA:9640" - }, { - "val" : "GAID:100" - }, { - "val" : "MA:0000011" - }, { - "val" : "MAT:0000301" - }, { - "val" : "MESH:D003238" - }, { - "val" : "MIAA:0000301" - }, { - "val" : "NCIT:C12374" - }, { - "val" : "SCTID:361919005" - }, { - "val" : "TAO:0001641" - }, { - "val" : "UMLS:C0009780" - }, { - "val" : "VSAO:0000017" - }, { - "val" : "XAO:0001017" - }, { - "val" : "ZFA:0001632" - }, { - "val" : "galen:ConnectiveTissue" + "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "lbl" : "muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", - "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, - "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus muscularis" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0000306" - }, { - "val" : "AEO:0000122" - }, { - "val" : "CALOHA:TS-0642" - }, { - "val" : "EHDAA2:0003122" - }, { - "val" : "EMAPA:32715" - }, { - "val" : "FMA:9641" - }, { - "val" : "MA:0002437" - }, { - "val" : "MESH:D009132" - }, { - "val" : "NCIT:C12435" - }, { - "val" : "SCTID:91727004" - }, { - "val" : "UMLS:C2328219" - }, { - "val" : "Wikipedia:Muscle_tissue" - }, { - "val" : "galen:MuscleTissue" + "val" : "RO:0002215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - 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This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011003" - }, { - "val" : "BILA:0000104" - }, { - "val" : "BTO:0005810" - }, { - "val" : "FMA:9825" - }, { - "val" : "GAID:328" - }, { - "val" : "MA:0002711" - }, { - "val" : "MESH:D007107" - }, { - "val" : "NCIT:C12735" - }, { - "val" : "SCTID:362590003" - }, { - "val" : "TAO:0001159" - }, { - "val" : "UMLS:C0020962" - }, { - "val" : "VHOG:0001247" - }, { - "val" : "Wikipedia:Immune_system" - }, { - "val" : "XAO:0003152" - }, { - "val" : "ZFA:0001159" + "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "lbl" : "bone tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000047", "http://dx.plos.org/10.1371/journal.pone.0051070" ] + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "calcium tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "osseous tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "osteogenic tissue", - "xrefs" : [ "VSAO:curator" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "mineralized bone tissue", - "xrefs" : [ "XAO:0004040" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "bone", - "xrefs" : [ "MESH:A02.835.232" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "portion of bone tissue", - "xrefs" : [ "FMA:224804" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "CALOHA:TS-2011" - }, { - "val" : "EMAPA:35179" - }, { - "val" : "FMA:224804" - }, { - "val" : "MA:0002780" - }, { - "val" : "MESH:D001842" - }, { - "val" : "NCIT:C13076" - }, { - "val" : "UMLS:C0391978" - }, { - "val" : "VSAO:0000047" - }, { - "val" : "Wikipedia:Bone_tissue" - }, { - "val" : "XAO:0004040" - }, { - "val" : "ZFA:0005621" - }, { - "val" : "galen:BoneTissue" + "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "see https://github.com/obophenotype/uberon/issues/27" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", - "lbl" : "epiblast (generic)", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", - "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] + "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epiblast", - "xrefs" : [ "VHOG:0000243" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocyst" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ectoblast", - "xrefs" : [ "MP:0003886" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epiblastus", - "xrefs" : [ "Wikipedia:Epiblast" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "primitive ectoderm", - "xrefs" : [ "VHOG:0000243" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BTO:0004593" - }, { - "val" : "FMA:296704" - }, { - "val" : "MAT:0000067" - }, { - "val" : "MIAA:0000067" - }, { - "val" : "VHOG:0000243" - }, { - "val" : "Wikipedia:Epiblast" + "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_start_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002232", + "lbl" : "has end location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] + "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" - }, { - "val" : "NCIT:C34007" - }, { - "val" : "galen:Cavity" + "val" : "RO:0002232" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_end_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002233", + "lbl" : "has input", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "segmental plate" - }, { - "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" - }, { - "val" : "XAO:0000057" - }, { - "val" : "ZFA:0000279" + "val" : "RO:0002233" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_input" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002234", + "lbl" : "has output", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", - "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] + "val" : "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ventral lateral plate mesoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "blood islands" - }, { - "pred" : "hasRelatedSynonym", - "val" : "VBI" - }, { - "pred" : "hasRelatedSynonym", - "val" : "caudal hematopoietic tissue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior ICM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior blood island" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral blood island" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011006" - }, { - "val" : "EFO:0003489" - }, { - "val" : "EHDAA:207" - }, { - "val" : "NCIT:C34113" - }, { - "val" : "TAO:0000094" - }, { - "val" : "TE:E5.11.2.0.0.0.4" - }, { - "val" : "UMLS:C1511224" - }, { - "val" : "VHOG:0000085" - }, { - "val" : "Wikipedia:Blood_island_of_umbilical_vesicle" - }, { - "val" : "XAO:0000067" - }, { - "val" : "ZFA:0000094" + "val" : "RO:0002234" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_output" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "lbl" : "axial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002252", + "lbl" : "connecting branch of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.", - "xrefs" : [ "GO:0048318", "Wikipedia:Chordamesoderm" ] + "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm", - "xrefs" : [ "Wikipedia:Chordamesoderm" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011017" - }, { - "val" : "EFO:0003647" - }, { - "val" : "TAO:0001204" - }, { - "val" : "VHOG:0000107" - }, { - "val" : "Wikipedia:Chordamesoderm" - }, { - "val" : "XAO:0000205" - }, { - "val" : "ZFA:0001204" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "lbl" : "neural plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002253", + "lbl" : "has connecting branch", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A region of embryonic ectodermal cells that lie directly above the notochord. 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"pred" : "hasRelatedSynonym", - "val" : "mesenchyma", - "xrefs" : [ "Wikipedia:Mesenchyme" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0010427" - }, { - "val" : "AEO:0000145" - }, { - "val" : "BTO:0001393" - }, { - "val" : "CALOHA:TS-0620" - }, { - "val" : "EHDAA2:0003145" - }, { - "val" : "EV:0100007" - }, { - "val" : "NCIT:C13301" - }, { - "val" : "TAO:0000393" - }, { - "val" : "UMLS:C0162415" - }, { - "val" : "VHOG:0000170" - }, { - "val" : "Wikipedia:Mesenchyme" - }, { - "val" : "XAO:0003046" - }, { - "val" : "ZFA:0000393" + "val" : "RO:0002305" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "lbl" : "future coelemic cavity lumen", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002314", + "lbl" : "characteristic of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future coelomic cavity lumen" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" }, { - "pred" : "hasRelatedSynonym", - "val" : "body cavity precursor" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002315", + "lbl" : "results in acquisition of features of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002315" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_acquisition_of_features_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", - "lbl" : "intraembryonic coelom", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002320", + "lbl" : "evolutionarily related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", - "xrefs" : [ "MGI:anna", "MP:0012187" ] + "val" : "A relationship that holds via some environmental process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002323", + "lbl" : "mereotopologically related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A mereological relationship or a topological relationship" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002324", + "lbl" : "developmentally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002328", + "lbl" : "functionally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002329", + "lbl" : "part of structure that is capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002330", + "lbl" : "genomically related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002332", + "lbl" : "regulates levels of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p regulates levels of c if p regulates some amount (PATO:0000070) of c" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "somatic coelom", - "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] - } ], "xrefs" : [ { - "val" : "EHDAA:251" - }, { - "val" : "EMAPA:16088" - }, { - "val" : "NCIT:C34195" - }, { - "val" : "UMLS:C1512940" - }, { - "val" : "VHOG:0000316" - }, { - "val" : "Wikipedia:Intraembryonic_coelom" + "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates_levels_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", - "lbl" : "epithelial tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002334", + "lbl" : "regulated by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", - "xrefs" : [ "GO:0060562", "PMID:12526790" ] + "val" : "inverse of regulates" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial or endothelial tube" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "xrefs" : [ { - "val" : "AEO:0000114" - }, { - "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" + "val" : "RO:0002334" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulated_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004111", - "lbl" : "anatomical conduit", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002335", + "lbl" : "negatively regulated by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any tube, opening or passage that connects two distinct anatomical spaces.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "inverse of negatively regulates" }, - 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}, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulated_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002336", + "lbl" : "positively regulated by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of positively regulates" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "xrefs" : [ { + "val" : "RO:0002336" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulated_by" } ] } }, { - 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"pred" : "hasExactSynonym", - "val" : "mesodermal derivative", - "xrefs" : [ "FBbt:00025998" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002338" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_start_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004121", - "lbl" : "ectoderm-derived structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002339", + "lbl" : "has target end location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical structure that develops (entirely or partially) from the ectoderm.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ectodermal deriviative", - "xrefs" : [ "FBbt:00025990" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002339" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_target_end_location" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", - "lbl" : "cardiogenic plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002341", + "lbl" : "results in transport along", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The first recognizable structure derived from the heart field.", - "xrefs" : [ "GO:0003142" ] + "val" : "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "myocardial plate", - "xrefs" : [ "EHDAA2:0000215" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac crescent", - "xrefs" : [ "EMAPA:16106" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiogenic crescent", - "xrefs" : [ "GO:0003142" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "heart rudiment" - } ], "xrefs" : [ { - "val" : "EHDAA2:0000215" - }, { - "val" : "EMAPA:16106" - }, { - "val" : "VHOG:0000975" + "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_along" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", - "lbl" : "primary heart field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002342", + "lbl" : "results in transport across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", - "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] + "val" : "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "first heart field", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primary heart field", - "xrefs" : [ "PMID:17276708", "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "FHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "PHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "heart field", - "xrefs" : [ "XAO:0004185" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_ontology" ], "xrefs" : [ { - "val" : "XAO:0004185" + "val" : "RO:0002342" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_across" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", - "lbl" : "heart tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002343", + "lbl" : "results in growth of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An epithelial tube that will give rise to the mature heart.", - "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic heart tube", - "xrefs" : [ "GO:0003143" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial heart tube", - "xrefs" : [ "MP:0012700" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial tube", - "xrefs" : [ "XAO:0000337" ] - } ], "xrefs" : [ { - "val" : "AAO:0010411" - }, { - "val" : "EFO:0003526" - }, { - "val" : "EMAPA:32685" - }, { - "val" : "NCIT:C34161" - }, { - "val" : "TAO:0000360" - }, { - "val" : "XAO:0000337" - }, { - "val" : "ZFA:0000360" + "val" : "RO:0002343" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_growth_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", - "lbl" : "cardiac chamber", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002344", + "lbl" : "results in transport to from or in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", - "xrefs" : [ "GO:0003205" ] - }, - "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chamber of heart" - }, { - "pred" : "hasExactSynonym", - "val" : "heart chamber" - } ], "xrefs" : [ { - "val" : "FMA:7095" - }, { - "val" : "SCTID:276456008" + "val" : "RO:0002344" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_transport_to_from_or_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002350", + "lbl" : "member of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "is member of is a mereological relation between a item and a collection." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002351", + "lbl" : "has member", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "has member is a mereological relation between a collection and an item." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002352", + "lbl" : "input of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "set of all bones" - }, { - "pred" : "hasExactSynonym", - "val" : "set of bones of body" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002353", + "lbl" : "output of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of has output" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AEO:0000168" - }, { - "val" : "EHDAA2:0001843" - }, { - "val" : "EHDAA:5047" - }, { - "val" : "EMAPA:17213" - }, { - "val" : "FMA:23875" - }, { - "val" : "GAID:177" - }, { - "val" : "MA:0003006" - }, { - "val" : "MAT:0000032" - }, { - "val" : "MESH:D012863" - }, { - "val" : "MIAA:0000032" - }, { - "val" : "SCTID:361378004" - }, { - "val" : "VSAO:0000026" - }, { - "val" : "Wikipedia:Skeleton" - }, { - "val" : "XAO:0004053" - }, { - "val" : "galen:Skeleton" + "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "output_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002354", + "lbl" : "formed as result of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002360", + "lbl" : "has dendrite location", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002371", + "lbl" : "attached to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002372", + "lbl" : "has muscle origin", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." + }, + "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" + "val" : "http://dbpedia.org/property/origin" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004291", - "lbl" : "heart rudiment", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002373", + "lbl" : "has muscle insertion", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.", - "xrefs" : [ "GO:0003313" ] + "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart cone", - "xrefs" : [ "GO:0003313" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rudimentary heart", - "xrefs" : [ "ZFA:0000115" ] - } ], - "xrefs" : [ { - "val" : "TAO:0000115" - }, { - "val" : "ZFA:0000115" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004535", - "lbl" : "cardiovascular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that has as its parts the heart and blood vessels.", - "xrefs" : [ "BTO:0000088" ] + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "CV system", - "xrefs" : [ "BTO:0000088" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Herz und Gefaesssystem", - "xrefs" : [ "BTO:0000088" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011001" - }, { - "val" : "BILA:0000016" - }, { - "val" : "BTO:0000088" - }, { - "val" : "CALOHA:TS-1297" - }, { - "val" : "EFO:0000791" - }, { - "val" : "EHDAA:394" - }, { - "val" : "EMAPA:16104" - }, { - "val" : "EV:0100017" - }, { - "val" : "FMA:7161" - }, { - "val" : "GAID:467" - }, { - "val" : "MA:0000010" - }, { - "val" : "MAT:0000016" - }, { - "val" : "MESH:D002319" - }, { - "val" : "MIAA:0000016" - }, { - "val" : "NCIT:C12686" - }, { - "val" : "SCTID:278198007" - }, { - "val" : "TAO:0000010" - }, { - "val" : "UMLS:C0007226" - }, { - "val" : "VHOG:0000302" - }, { - "val" : "WikipediaCategory:Cardiovascular_system" - }, { - "val" : "XAO:0000100" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { - "val" : "XAO:0001010" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" }, { - "val" : "ZFA:0000010" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004537", - "lbl" : "blood vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A vascular network consisting of blood vessels.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "inverse of upstream of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blood vascular network" - }, { - "pred" : "hasExactSynonym", - "val" : "set of blood vessels" - }, { - "pred" : "hasRelatedSynonym", - "val" : "blood system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "blood vessel system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "blood vessels", - "xrefs" : [ "TAO:0001079" ] - } ], "xrefs" : [ { - "val" : "TAO:0001079" - }, { - "val" : "ZFA:0001079" + "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004638", - "lbl" : "blood vessel endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "xrefs" : [ { - "val" : "BTO:0000766" - }, { - "val" : "CALOHA:TS-2155" - }, { - "val" : "EMAPA:35176" - }, { - "val" : "MA:0000709" - }, { - "val" : "NCIT:C53395" - }, { - "val" : "TAO:0005257" - }, { - "val" : "UMLS:C1706972" - }, { - "val" : "ZFA:0005257" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004716", - "lbl" : "conceptus", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].", - "xrefs" : [ "BTO:0003834", "Wikipedia:Conceptus" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryo plus adnexa" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AEO:0000194" - }, { - "val" : "BTO:0003834" - }, { - "val" : "EHDAA2:0000001" - }, { - "val" : "EHDAA2:0003235" - }, { - "val" : "EMAPA:36040" - }, { - "val" : "NCIT:C34131" - }, { - "val" : "UMLS:C1516779" - }, { - "val" : "Wikipedia:Conceptus" + "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", - "lbl" : "gastrula", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the gastrula stage.", - "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gastrula embryo", - "xrefs" : [ "BILA:0000060" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocystis trilaminaris", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastocyst", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "trilaminar germ", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "BILA:0000060" - }, { - "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" - }, { - "val" : "FMA:293108" - }, { - "val" : "GAID:1302" - }, { - "val" : "MESH:D005775" - }, { - "val" : "MIAA:0000179" - }, { - "val" : "NCIT:C34057" - }, { - "val" : "NCIT:C34058" - }, { - "val" : "UMLS:C0017199" - }, { - "val" : "UMLS:C1284022" - }, { - "val" : "Wikipedia:Gastrula" - }, { - "val" : "Wikipedia:Trilaminar_blastocyst" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004755", - "lbl" : "skeletal tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000015", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/134" ] + "val" : "inverse of causally upstream of or within" }, - "comments" : [ "Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from" ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "xrefs" : [ { - "val" : "EMAPA:37744" - }, { - "val" : "MA:0003047" - }, { - "val" : "SCTID:309311006" - }, { - "val" : "VSAO:0000015" - }, { - "val" : "XAO:0004038" - }, { - "val" : "ZFA:0005619" + "val" : "RO:0002427" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", - "lbl" : "skeletal element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" - }, { - "val" : "galen:SkeletalStructure" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" - }, { - "val" : "MA:0003007" - }, { - "val" : "SCTID:361827000" - }, { - "val" : "VSAO:0000181" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", - "lbl" : "cardiovascular system endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that is part of the cardiovascular system.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "endothelia", - "xrefs" : [ "ZFA:0001639" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "vascular endothelia", - "xrefs" : [ "XAO:0000356" ] - } ], - "xrefs" : [ { - "val" : "BTO:0001853" - }, { - "val" : "EMAPA:35201" - }, { - "val" : "GAID:519" - }, { - "val" : "MA:0000717" - }, { - "val" : "MESH:D004730" - }, { - "val" : "NCIT:C13053" - }, { - "val" : "TAO:0002171" - }, { - "val" : "UMLS:C0014261" - }, { - "val" : "VHOG:0001217" - }, { - "val" : "XAO:0000356" - }, { - "val" : "ZFA:0001639" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004872", - "lbl" : "splanchnic layer of lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "visceral mesoderm", - "xrefs" : [ "BILA:0000044", "http://www.drugs.com/dict/visceral-mesoderm.html", "http://www.stedmans.com/" ] - }, { - "pred" : "hasExactSynonym", - "val" : "inner layer of lateral plate mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011102" - }, { - "val" : "BILA:0000044" - }, { - "val" : "FMA:295568" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" - }, { - "val" : "XAO:0000276" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000478" - }, { - "val" : "EFO:0003426" - }, { - "val" : "TAO:0000091" - }, { - "val" : "ZFA:0000091" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004905", - "lbl" : "articulation", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A proximal-distal subdivision of the digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system subdivision", - "xrefs" : [ "FMA:71131" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut section", - "xrefs" : [ "FBbt:00100315" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "segment of intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "subdivision of alimentary system", - "xrefs" : [ "FMA:71131" ] - } ], - "xrefs" : [ { - "val" : "FBbt:00100315" - }, { - "val" : "FMA:71131" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "lbl" : "organ component layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A part of a wall of an organ that forms a layer.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FMA:82485" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "exists during" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005061", - "lbl" : "neural groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.", - "xrefs" : [ "GO:0001842", "Wikipedia:Neural_groove", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. 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The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "lbl" : "neural fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "One of the two elevated edges of the neural groove[GO,MP].", - "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. 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X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", - "lbl" : "meso-epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesoderm-derived epithelium" - }, { - "pred" : "hasExactSynonym", - "val" : "mesoepithelium" - } ], - "xrefs" : [ { - "val" : "FMA:86452" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012429", - "lbl" : "hematopoietic tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", + "lbl" : "transitively distally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Blood-forming tissue, consisting of reticular fibers and cells.", - "xrefs" : [ "http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue" ] - 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Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", - "lbl" : "body proper", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "The region of the organism associated with the visceral organs.", - "xrefs" : [ "AEO:0000103" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "body", - "xrefs" : [ "AEO:0000103" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "whole body", - "xrefs" : [ "BTO:0001489" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000103" - }, { - "val" : "BTO:0001489" - }, { - "val" : "FMA:231424" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", - "lbl" : "thoracic skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", - "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "skeleton of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic part of axial skeleton" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic skeleton", - "xrefs" : [ "EHDAA2:0002013" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002013" - }, { - "val" : "FMA:77169" - }, { - "val" : "Wikipedia:Thoracic_skeleton" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", - "lbl" : "primordial vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A portion of tissue that will develop into vasculature.", - "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "xrefs" : [ { - "val" : "EFO:0003708" - }, { - "val" : "TAO:0005076" - }, { - "val" : "ZFA:0005076" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015203", - "lbl" : "non-connected functional system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An anatomical group whose component structures share a common function.", - "xrefs" : [ "AEO:0000093", "AEO:JB", "FBC:DOS", "FBbt:00007278" ] + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, - "xrefs" : [ { - "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "lbl" : "lateral structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", - "lbl" : "circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "heart" - }, { - "pred" : "hasExactSynonym", - "val" : "cardiac pump" - }, { - "pred" : "hasExactSynonym", - "val" : "heart or heart like organ" - }, { - "pred" : "hasNarrowSynonym", - "val" : "circulatory vessel" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac structure" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", - "lbl" : "heart plus pericardium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart/pericardium", - "xrefs" : [ "MA:0002449" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37597" - }, { - "val" : "MA:0002449" - } ], + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015757", - "lbl" : "heterogeneous tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of heterogeneous tissue", - "xrefs" : [ "FMA:62798" ] - } ], - "xrefs" : [ { - "val" : "FMA:62798" - } ], + "definition" : { + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", - "lbl" : "future central nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Primordium that develops into the central nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future CNS" - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive central nervous system" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", - "lbl" : "future nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Primordium that develops into the nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive nervous system", - "xrefs" : [ "AAO:0000477" ] - } ], + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "xrefs" : [ { - "val" : "AAO:0000477" + "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016887", - "lbl" : "entire extraembryonic component", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", - "xrefs" : [ "AEO:0000195", "AEO:JB" ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "extra-embryonic component" - }, { - "pred" : "hasExactSynonym", - "val" : "extraembryonic component", - "xrefs" : [ "AEO:0000195" ] - } ], "xrefs" : [ { - "val" : "AEO:0000195" - }, { - "val" : "EHDAA2:0000003" - }, { - "val" : "EMAPA:16042" + "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034769", - "lbl" : "lymphomyeloid tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "xrefs" : [ { - "val" : "FMA:79770" - }, { - "val" : "NCIT:C41168" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" + }, + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], - "xrefs" : [ { - "val" : "CARO:0020001" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] + "val" : "A synonym type for describing abbreviations or initalisms" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A synonym type for describing pluralization synonyms" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], - "xrefs" : [ { - "val" : "FMA:293105" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036146", - "lbl" : "cardiopharyngeal field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.", - "xrefs" : [ "http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1", "https://orcid.org/0000-0003-3308-6245" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { @@ -31460,6 +31957,7 @@ "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } @@ -31467,49 +31965,15 @@ "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { @@ -31517,291 +31981,391 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", "lbl" : "latin term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", "lbl" : "plural term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "type" : "PROPERTY", - "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." - }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "type" : "PROPERTY", - "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -31817,11 +32381,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -31838,6 +32404,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -31853,11 +32420,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -31873,23 +32442,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -31899,6 +32497,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -32134,16 +32744,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000483" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000076", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "is_a", @@ -32392,8 +32992,8 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000213" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000133", "pred" : "is_a", @@ -34416,14 +35016,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002077", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000221" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002078", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000066" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002078", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002087", "pred" : "is_a", @@ -35994,10 +36586,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044249" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009059", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_1901576" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009605", "pred" : "is_a", @@ -37778,10 +38366,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0070925", "pred" : "http://purl.obolibrary.org/obo/RO_0002588", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0071704", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0071707", "pred" : "is_a", @@ -38138,14 +38722,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140546", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0098542" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1902105", "pred" : "is_a", @@ -38582,6 +39158,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070047", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0070045" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -38926,6 +39514,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000040662", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000025", "pred" : "is_a", @@ -43232,6 +43824,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -43334,10 +43930,10 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000071", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000076" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0004638" + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000080", @@ -44559,13 +45155,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000221" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002078", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", - "fillerId" : "http://purl.obolibrary.org/obo/CL_0000222" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0002087", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000738" ], @@ -46850,6 +47439,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/subsets/blood_and_immune_upper_slim.obo b/subsets/blood_and_immune_upper_slim.obo index 5f0fdb066..ad7ec0937 100644 --- a/subsets/blood_and_immune_upper_slim.obo +++ b/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -119,7 +124,7 @@ relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] @@ -133,7 +138,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -158,7 +163,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -206,7 +211,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -222,7 +227,7 @@ synonym: "colony forming unit monocyte" RELATED [] synonym: "monocyte stem cell" RELATED [] xref: CALOHA:TS-1195 xref: FMA:83553 -xref: ZFA:0009017 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -246,7 +251,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -269,7 +274,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor @@ -290,7 +295,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -319,7 +324,7 @@ synonym: "early lymphocyte progenitor" RELATED [] synonym: "ELP" RELATED OMO:0003000 [] synonym: "lymphoid stem cell" RELATED [] synonym: "lymphopoietic stem cell" RELATED [] -xref: ZFA:0009023 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009023 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell @@ -334,7 +339,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -354,10 +359,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -373,7 +378,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -389,14 +394,14 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -405,12 +410,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -420,14 +423,14 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] -xref: ZFA:0009043 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid @@ -441,7 +444,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -464,7 +467,7 @@ xref: CALOHA:TS-1001 xref: FMA:62870 xref: MESH:D013601 xref: VHOG:0001479 -xref: ZFA:0009046 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009046 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000542 {is_inferred="true"} ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity @@ -484,7 +487,7 @@ xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 xref: MESH:D010010 -xref: ZFA:0009047 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell @@ -521,7 +524,7 @@ xref: BTO:0000539 xref: BTO:0001026 xref: CALOHA:TS-0422 xref: FMA:62854 -xref: ZFA:0009048 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte @@ -596,7 +599,7 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 -xref: ZFA:0009064 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) @@ -614,9 +617,9 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -624,7 +627,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -648,7 +651,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -661,7 +664,7 @@ comment: Note change of name; nearly all somatic cells can present antigens to T subset: blood_and_immune_upper_slim subset: cellxgene_subset synonym: "APC" RELATED OMO:0003000 [] -xref: ZFA:0009088 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II @@ -696,20 +699,20 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -717,21 +720,21 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -743,7 +746,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -755,7 +758,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -765,7 +768,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -862,7 +865,7 @@ subset: cellxgene_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 -xref: ZFA:0009140 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009140 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000473 ! defensive cell @@ -885,7 +888,7 @@ xref: CALOHA:TS-0587 xref: FMA:63261 xref: FMA:83585 xref: MESH:D008264 -xref: ZFA:0009141 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009141 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte @@ -913,7 +916,7 @@ xref: CALOHA:TS-0068 xref: FMA:62869 xref: MESH:D001402 xref: VHOG:0001480 -xref: ZFA:0009142 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009142 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity @@ -942,7 +945,7 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -953,7 +956,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -963,7 +966,7 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -991,14 +994,14 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1014,7 +1017,7 @@ xref: BTO:0002042 xref: CALOHA:TS-0194 xref: FMA:83036 xref: MESH:D003713 -xref: ZFA:0009209 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell intersection_of: CL:0000738 ! leukocyte @@ -1043,7 +1046,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000457 name: biogenic amine secreting cell -xref: ZFA:0009212 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009212 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell [Term] @@ -1052,7 +1055,7 @@ name: serotonin secreting cell def: "A cell type that secretes 5-Hydroxytryptamine (serotonin)." [GOC:tfm, PMID:19630576] synonym: "5-HT secreting cell" EXACT [] synonym: "5-Hydroxytryptamine secreting cell" EXACT [] -xref: ZFA:0009213 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009213 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001820 ! serotonin secretion @@ -1083,16 +1086,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1107,7 +1110,7 @@ xref: CALOHA:TS-0583 xref: FMA:62863 xref: MESH:D008214 xref: VHOG:0001535 -xref: ZFA:0009250 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009250 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -1175,7 +1178,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -1196,7 +1199,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -1314,7 +1317,7 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] -xref: ZFA:0009251 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell @@ -1346,7 +1349,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -1386,7 +1389,7 @@ subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0004657 xref: FMA:83551 -xref: ZFA:0009253 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -1405,7 +1408,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1429,7 +1432,7 @@ subset: human_reference_atlas xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 -xref: ZFA:0009265 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009265 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0011026 ! progenitor cell @@ -1473,7 +1476,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1486,7 +1489,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1506,7 +1509,7 @@ xref: CALOHA:TS-0549 xref: FMA:62852 xref: MESH:D007962 xref: NCIT:C12529 -xref: ZFA:0009309 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009309 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell @@ -1526,7 +1529,7 @@ name: nucleated thrombocyte def: "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:16360205] comment: Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. subset: blood_and_immune_upper_slim -xref: ZFA:0009323 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell intersection_of: CL:0000763 ! myeloid cell @@ -1543,7 +1546,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1560,7 +1563,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -1575,7 +1578,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -1614,7 +1617,7 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009326 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte @@ -1704,7 +1707,7 @@ xref: BTO:0000130 xref: CALOHA:TS-0688 xref: FMA:62860 xref: MESH:D009504 -xref: ZFA:0009327 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009327 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II @@ -1764,7 +1767,7 @@ subset: cellxgene_subset synonym: "mature B lymphocyte" EXACT [] synonym: "mature B-cell" EXACT [] synonym: "mature B-lymphocyte" EXACT [] -xref: ZFA:0009331 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009331 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive @@ -1795,7 +1798,7 @@ synonym: "plasmocyte" EXACT [] xref: BTO:0000392 xref: FMA:70574 xref: MESH:D010950 -xref: ZFA:0009332 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex @@ -1822,7 +1825,7 @@ subset: cellxgene_subset synonym: "alpha-beta T lymphocyte" EXACT [] synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] -xref: ZFA:0009335 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex @@ -1842,7 +1845,7 @@ synonym: "gamma-delta T-cell" EXACT [] synonym: "gamma-delta T-lymphocyte" EXACT [] synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] -xref: ZFA:0009336 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -1861,7 +1864,7 @@ synonym: "immature B lymphocyte" EXACT [] synonym: "immature B-cell" EXACT [] synonym: "immature B-lymphocyte" EXACT [] synonym: "newly formed B cell" EXACT [ISBN:781735149] -xref: ZFA:0009343 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009343 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030044 GO:0045190 ! has_not_completed isotype switching @@ -1884,7 +1887,7 @@ subset: human_reference_atlas synonym: "pre-B cell" RELATED [] xref: BTO:0001133 xref: CALOHA:TS-0819 -xref: ZFA:0009344 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009344 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex @@ -1908,7 +1911,7 @@ synonym: "transitional B cell" EXACT [PMID:22343568] synonym: "transitional stage B lymphocyte" EXACT [] synonym: "transitional stage B-cell" EXACT [] synonym: "transitional stage B-lymphocyte" EXACT [] -xref: ZFA:0009345 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009345 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001201 {is_inferred="true"} ! B cell, CD19-positive intersection_of: CL:0001201 ! B cell, CD19-positive intersection_of: CL:4030044 GO:0002335 ! has_not_completed mature B cell differentiation @@ -1941,7 +1944,7 @@ synonym: "progenitor B lymphocyte" EXACT [] synonym: "progenitor B-cell" EXACT [] synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 -xref: ZFA:0009349 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 @@ -1963,7 +1966,7 @@ synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] synonym: "progenitor T cell" EXACT [] synonym: "TN1 cell" NARROW [] -xref: ZFA:0009350 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009350 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation @@ -1975,7 +1978,7 @@ id: CL:0000828 name: thromboblast def: "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." [GOC:add, GOC:tfm, PMID:7758949] comment: Note that this is a non-mammalian cell type. -xref: ZFA:0009351 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009351 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell @@ -2059,7 +2062,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -2106,7 +2109,7 @@ synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 xref: FMA:70338 -xref: ZFA:0009355 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009355 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -2125,7 +2128,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -2144,7 +2147,7 @@ synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 xref: CALOHA:TS-0768 xref: FMA:86713 -xref: ZFA:0009357 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009357 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte @@ -2261,7 +2264,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -2301,8 +2304,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 creation_date: 2011-11-16T04:28:16Z [Term] @@ -2336,7 +2339,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2356,9 +2359,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:20:48Z" xsd:dateTime [Term] id: CL:0001200 @@ -2373,7 +2376,7 @@ intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001201 @@ -2390,7 +2393,7 @@ intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0002009 @@ -2407,7 +2410,7 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -2437,7 +2440,7 @@ relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T12:46:33Z [Term] @@ -2451,7 +2454,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -2465,7 +2468,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2473,28 +2476,14 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z -[Term] -id: CL:0002078 -name: meso-epithelial cell -def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] -synonym: "epithelial mesenchymal cell" EXACT [] -xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000066 ! epithelial cell -intersection_of: CL:0000066 ! epithelial cell -intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell -relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2010-06-29T03:49:14Z - [Term] id: CL:0002087 name: nongranular leukocyte @@ -2506,7 +2495,7 @@ is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: CL:4030045 GO:0030141 ! lacks_part secretory granule relationship: CL:4030045 GO:0030141 ! lacks_part secretory granule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T11:30:33Z [Term] @@ -2522,7 +2511,7 @@ is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -2537,7 +2526,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -2550,7 +2539,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T12:54:27Z [Term] @@ -2562,7 +2551,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -2574,7 +2563,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -2585,7 +2574,7 @@ is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion relationship: capable_of GO:0001821 ! histamine secretion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:04:42Z [Term] @@ -2599,7 +2588,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -2610,12 +2599,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -2625,9 +2614,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -2643,7 +2632,7 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0045058 ! has_not_completed T cell selection -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:17Z [Term] @@ -2660,7 +2649,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -2668,9 +2657,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -2700,7 +2689,7 @@ relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like pr relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-29T10:08:02Z [Term] @@ -2710,18 +2699,18 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2768,7 +2757,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2791,7 +2780,7 @@ xref: EFO:0000572 xref: FMA:83030 is_a: CL:0000542 ! lymphocyte relationship: output_of GO:0046649 ! lymphocyte activation -property_value: http://purl.org/dc/elements/1.1/date "2022-08-17T14:20:01Z" xsd:string +property_value: dc:date "2022-08-17T14:20:01Z" xsd:string created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -2803,7 +2792,7 @@ xref: EFO:0005293 xref: FMA:83031 is_a: CL:0000945 ! lymphocyte of B lineage is_a: CL:0017005 ! lymphoblast -property_value: http://purl.org/dc/elements/1.1/date "2022-08-17T14:30:32Z" xsd:string +property_value: dc:date "2022-08-17T14:30:32Z" xsd:string created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -2814,7 +2803,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2826,7 +2815,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2837,7 +2826,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2848,7 +2837,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2856,7 +2845,7 @@ id: CL:0017508 name: cartwheel heterochromatin def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:28:35Z [Term] @@ -2882,7 +2871,7 @@ is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0000178 ! blood relationship: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-11T17:29:04Z [Term] @@ -2894,14 +2883,14 @@ is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood -property_value: http://purl.org/dc/terms/date "2022-11-04T14:40:00Z" xsd:dateTime +property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -3928,7 +3917,7 @@ alt_id: GO:0001623 alt_id: GO:0001624 alt_id: GO:0001625 alt_id: GO:0016526 -def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, http://www.iuphar-db.org, Wikipedia:GPCR] +def: "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, Wikipedia:GPCR] subset: goslim_chembl synonym: "EBV-induced receptor" NARROW [] synonym: "Epstein-Barr Virus-induced receptor activity" NARROW [] @@ -4459,7 +4448,7 @@ name: exocytosis namespace: biological_process alt_id: GO:0016194 alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] +def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] synonym: "vesicle exocytosis" EXACT [] @@ -4998,7 +4987,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -5606,7 +5594,7 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -5621,7 +5609,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -5634,7 +5622,7 @@ relationship: results_in_assembly_of GO:0042995 ! cell projection id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -6610,7 +6598,7 @@ is_a: GO:0042611 ! MHC protein complex id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -6842,13 +6830,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -7961,20 +7950,6 @@ relationship: results_in_assembly_of GO:0043226 ! organelle created_by: mah creation_date: 2009-09-15T03:00:51Z -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071707 name: immunoglobulin heavy chain V-D-J recombination @@ -8504,27 +8479,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2020-11-11T17:19:06Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1902105 name: regulation of leukocyte differentiation @@ -9325,7 +9279,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -9335,7 +9289,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -9347,7 +9301,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -9357,7 +9311,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -9366,7 +9320,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -9379,7 +9333,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -9389,7 +9343,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -9402,7 +9356,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -9413,7 +9367,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -9422,7 +9376,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -9484,6 +9438,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -10592,6 +10549,15 @@ synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -10648,6 +10614,18 @@ synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -10718,7 +10696,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -11024,7 +11002,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -11126,7 +11104,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -11150,7 +11128,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -11209,7 +11187,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -11232,7 +11210,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -11292,7 +11270,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -11327,7 +11305,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -11355,7 +11333,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -11380,7 +11358,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -11417,7 +11395,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -11471,7 +11449,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -11515,7 +11493,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -11551,7 +11529,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -11571,7 +11549,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -11598,7 +11576,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -11633,7 +11611,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -11666,7 +11644,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -11687,7 +11665,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -11716,7 +11694,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000490 @@ -11787,7 +11765,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -11808,7 +11786,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -11828,7 +11806,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -11862,7 +11840,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -11880,7 +11858,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -11900,7 +11878,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -11917,8 +11895,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -11944,7 +11922,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -11961,7 +11939,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -11984,7 +11962,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -11997,7 +11975,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -12052,9 +12030,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -12119,7 +12097,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -12169,7 +12147,7 @@ disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -12208,7 +12186,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -12234,7 +12212,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -12262,8 +12240,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -12294,7 +12272,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -12334,7 +12312,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -12381,7 +12359,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -12397,7 +12375,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -12522,7 +12500,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -12653,7 +12631,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -12702,7 +12680,7 @@ is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -12724,7 +12702,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -12916,8 +12894,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -12941,7 +12919,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12998,7 +12976,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -13039,7 +13017,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -13081,8 +13059,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -13105,7 +13083,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -13163,7 +13141,7 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -13364,7 +13342,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -13463,7 +13441,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -13498,7 +13476,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -13529,7 +13507,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -13564,7 +13542,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13614,7 +13592,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -13670,7 +13648,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -13716,7 +13694,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -13952,8 +13930,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -14018,7 +13996,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14158,7 +14136,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14174,7 +14152,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -14360,7 +14338,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -14464,7 +14442,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -14865,7 +14843,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -14949,7 +14927,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -15069,7 +15047,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -15255,7 +15233,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -15376,7 +15354,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -16489,8 +16467,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16498,8 +16476,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16508,8 +16486,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -16660,16 +16638,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -16678,6 +16660,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -16695,6 +16678,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -16913,6 +16897,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -17371,18 +17356,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/subsets/blood_and_immune_upper_slim.owl b/subsets/blood_and_immune_upper_slim.owl index 2a51bb253..bb770b572 100644 --- a/subsets/blood_and_immune_upper_slim.owl +++ b/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4511,6 +4517,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4522,6 +4530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4532,6 +4541,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4544,6 +4554,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4562,6 +4573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4591,6 +4603,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4699,6 +4712,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4710,6 +4724,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4721,6 +4736,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -5710,15 +5726,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - @@ -5735,17 +5750,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -6468,7 +6476,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -12441,7 +12454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A connective tissue cell found in bone. - 2011-11-16T04:28:16Z + 2011-11-16T04:28:16Z bone cell @@ -12593,7 +12606,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative @@ -12816,7 +12829,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. - 2010-01-19T02:51:58Z + 2010-01-19T02:51:58Z MDP macrophage dendritic cell progenitor @@ -12937,7 +12950,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa - 2010-04-27T12:46:33Z + 2010-04-27T12:46:33Z BMCP There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. @@ -12985,7 +12998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -13028,7 +13041,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -13067,7 +13080,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -13088,51 +13101,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - Epithelial cell derived from mesoderm or mesenchyme. - - 2010-06-29T03:49:14Z - FMA:69076 - ZFA:0009388 - epithelial mesenchymal cell - meso-epithelial cell - - - - - Epithelial cell derived from mesoderm or mesenchyme. - FMA:69076 - GOC:tfm - - - - - ZFA:0009388 - - - - - @@ -13156,7 +13124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A leukocyte that lacks granules. - 2010-07-22T11:30:33Z + 2010-07-22T11:30:33Z FMA:62855 agranular leukocyte @@ -13200,7 +13168,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. - 2010-07-22T04:48:15Z + 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 @@ -13230,7 +13198,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -13274,7 +13242,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell involved in the formation of a granulocyte. - 2010-08-30T12:54:27Z + 2010-08-30T12:54:27Z FMA:83519 granulocytopoietic cell @@ -13317,7 +13285,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell involved in the formation of a monocyte (monopoiesis). - 2010-08-30T01:27:48Z + 2010-08-30T01:27:48Z FMA:83552 monopoietic cell @@ -13359,7 +13327,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -13395,7 +13363,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell type that secretes histamine. - 2010-09-10T03:04:42Z + 2010-09-10T03:04:42Z histamine secreting cell @@ -13430,7 +13398,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -13469,7 +13437,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -13499,7 +13467,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -13544,7 +13512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A T cell that has not completed T cell selection. - 2010-10-12T01:56:17Z + 2010-10-12T01:56:17Z BTO:0001372 CALOHA:TS-1042 immature T-cell @@ -13590,7 +13558,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -13614,7 +13582,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -13747,7 +13715,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13 - 2011-08-29T10:08:02Z + 2011-08-29T10:08:02Z natural helper lymphocyte @@ -13773,7 +13741,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). - 2012-06-15T02:51:27Z + 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -13811,7 +13779,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -14050,7 +14018,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. - 2010-05-25T01:36:34Z + 2010-05-25T01:36:34Z neutrophillic cytoplasm @@ -14085,7 +14053,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -14121,7 +14089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -14156,7 +14124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -14174,7 +14142,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Heterochromatin that is arranged in a carthwheel pattern. - 2009-12-28T04:28:35Z + 2009-12-28T04:28:35Z cartwheel heterochromatin @@ -14258,8 +14226,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. - - 2014-02-11T17:29:04Z + + 2014-02-11T17:29:04Z CL:2000001 peripheral blood mononuclear cell @@ -14355,7 +14323,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 - Reactome:69278 @@ -17325,7 +17292,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex. GOC:bf Wikipedia:GPCR - http://www.iuphar-db.org @@ -17458,32 +17424,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -18407,7 +18373,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0016194 GO:0016195 Wikipedia:Exocytosis @@ -18421,7 +18387,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GOC:mah ISBN:0716731363 PMID:22323285 @@ -19662,7 +19628,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -21234,7 +21199,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -21286,7 +21251,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:18391171 @@ -21321,7 +21286,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -23996,7 +23960,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -24561,6 +24525,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite primary metabolism biological_process GO:0044238 @@ -24576,7 +24541,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators - http://www.metacyc.org @@ -27603,31 +27567,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism - biological_process - GO:0071704 - - organic substance metabolic process - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - GOC:mah - - - - @@ -29157,63 +29096,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -31497,6 +31379,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -34411,6 +34301,39 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -34616,6 +34539,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -35469,7 +35444,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35505,14 +35480,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -35828,15 +35803,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -35873,34 +35848,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -36985,7 +36960,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37027,14 +37002,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -37454,7 +37429,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -37489,14 +37464,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -37536,7 +37511,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -37571,14 +37546,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -37619,7 +37594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -37660,14 +37635,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -37841,7 +37816,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37913,14 +37888,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -38323,7 +38298,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38373,14 +38348,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -38446,7 +38421,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -38491,7 +38466,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -38505,7 +38480,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -38893,7 +38868,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Skeletal element that is composed of bone tissue. @@ -38935,14 +38910,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -39008,7 +38983,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -39045,14 +39020,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -39279,8 +39254,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -39293,7 +39268,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39347,34 +39322,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -40208,9 +40183,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40258,15 +40233,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -40285,19 +40260,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -40337,8 +40312,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -40376,11 +40351,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -40393,13 +40368,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -40461,22 +40436,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -40509,45 +40484,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -40688,7 +40663,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40744,14 +40719,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -40963,7 +40938,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41016,14 +40991,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -41336,7 +41311,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -41359,14 +41334,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -41520,9 +41495,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -41551,34 +41526,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -41618,7 +41593,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -41644,7 +41619,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41657,7 +41632,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -41704,7 +41679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41744,7 +41719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41757,7 +41732,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -41807,15 +41782,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -41832,15 +41807,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -41853,19 +41828,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -41894,8 +41869,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -41919,11 +41894,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -41942,13 +41917,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -42167,7 +42142,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -42182,14 +42157,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -42484,8 +42459,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -42497,24 +42472,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -42567,7 +42542,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -42586,14 +42561,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -43217,7 +43192,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -43231,14 +43206,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -43265,7 +43240,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43304,14 +43279,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -44025,7 +44000,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44041,14 +44016,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -44165,7 +44140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44183,14 +44158,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -44356,7 +44331,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44366,7 +44341,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -44385,7 +44360,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -44479,7 +44454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44493,7 +44468,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -44506,7 +44481,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -44534,7 +44509,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44551,14 +44526,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45447,7 +45422,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45473,7 +45448,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -45489,7 +45464,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -45565,7 +45540,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -45573,7 +45548,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -45586,7 +45561,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -45689,7 +45664,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -45706,14 +45681,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -45741,7 +45716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45758,14 +45733,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45821,7 +45796,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45829,14 +45804,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45859,7 +45834,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45869,14 +45844,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -46015,7 +45990,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46035,14 +46010,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010210 blood clot - + - + BTO @@ -46163,8 +46138,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46176,11 +46151,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -46193,13 +46168,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46260,7 +46235,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46270,7 +46245,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46283,7 +46258,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46556,7 +46531,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46577,7 +46552,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -46590,7 +46565,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -47141,7 +47116,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47164,7 +47139,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47177,7 +47152,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47701,5 +47676,5 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + diff --git a/subsets/blood_and_immune_upper_slim.tsv b/subsets/blood_and_immune_upper_slim.tsv index 42e83f39e..a99388ad7 100644 --- a/subsets/blood_and_immune_upper_slim.tsv +++ b/subsets/blood_and_immune_upper_slim.tsv @@ -1,388 +1,387 @@ ?x ?label 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+_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid608 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid618 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid653 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid667 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid683 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid70 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid73 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid736 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid754 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid775 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid790 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid845 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid877 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid922 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid936 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid951 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid968 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid986 +_:B2a27bc0cX2Df409X2D41c0X2D8ca4X2Da5582a4c2dbcgenid994 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -504,7 +503,6 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "hematopoietic lineage restricted progenitor cell" "hematopoietic oligopotent progenitor cell" "ecto-epithelial cell" - "meso-epithelial cell" "nongranular leukocyte" "bone marrow cell" "endothelial cell of vascular tree" @@ -908,7 +906,6 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "exocytic vesicle" "cellular response to chemical stimulus" "organelle assembly" - "organic substance metabolic process" "immunoglobulin heavy chain V-D-J recombination" "immunoglobulin light chain V-J recombination" "IgD immunoglobulin complex" @@ -952,7 +949,6 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "extracellular vesicle biogenesis" "export from cell" "defense response to symbiont" - "organic substance biosynthetic process" "regulation of leukocyte differentiation" "mitotic cell cycle process" "mononuclear cell differentiation" @@ -1125,11 +1121,13 @@ _:B4defd537X2De6edX2D485bX2Db68aX2Dd3a13531e3cbgenid994 "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" "transmembrane emp24 domain-containing protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "G-protein coupled receptor" "eukaryotic protein" "cathepsin-like protease" + "protein-containing molecular entity" "processual entity" "tube" "vessel" diff --git a/subsets/eye_upper_slim.json b/subsets/eye_upper_slim.json index 8ad22264c..c7df74eb0 100644 --- a/subsets/eye_upper_slim.json +++ b/subsets/eye_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/eye_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -657,10 +504,6 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cuboidal endothelial cell of vascular tree" - } ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -3364,7 +3207,7 @@ }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://www.wikidata.org/entity/Q35563349" + "val" : "http://www.wikidata.org/entity/Q35563349" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2014-06-25T01:17:43Z" @@ -3393,30 +3236,6 @@ "val" : "https://orcid.org/0000-0002-0819-0473" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_4033015", "lbl" : "retinal astrocyte", @@ -3442,38 +3261,6 @@ "val" : "2023-03-02T14:38:32Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -3481,7 +3268,7 @@ "meta" : { "definition" : { "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", - "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + "xrefs" : [ "GOC:mah", "ISBN:0815316194" ] }, "comments" : [ "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -6343,7 +6130,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -6373,7 +6160,7 @@ "meta" : { "definition" : { "val" : "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:18391171" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6395,7 +6182,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -7287,7 +7074,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -7312,7 +7099,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:3077060" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { @@ -7795,13 +7582,16 @@ "meta" : { "definition" : { "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", - "xrefs" : [ "GOC:go_curators", "http://www.metacyc.org" ] + "xrefs" : [ "GOC:go_curators" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "primary metabolism" } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" @@ -8647,7 +8437,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.", + "val" : "Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.", "xrefs" : [ "GOC:ai", "GOC:dos", "GOC:dph", "GOC:tb" ] }, "synonyms" : [ { @@ -9100,40 +8890,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071704", - "lbl" : "organic substance metabolic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance metabolism" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "mah" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-03-08T03:32:18Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0071826", "lbl" : "protein-RNA complex organization", @@ -9896,62 +9652,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1903047", "lbl" : "mitotic cell cycle process", @@ -10069,260 +9769,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], - "xrefs" : [ { - "val" : "IAO:0000233" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." - }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -10991,73 +10437,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -13132,6 +12511,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -13187,3109 +12590,6558 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000053" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000019", + "lbl" : "camera-type eye", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + "val" : "An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.", + "xrefs" : [ "GO:0043010", "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "eye", + "xrefs" : [ "FMA:54448" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio orbitalis", + "xrefs" : [ "FMA:54448", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "vertebrate eye" + }, { + "pred" : "hasRelatedSynonym", + "val" : "camera-type eye plus associated structures" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "eyes", + "xrefs" : [ "TAO:0000107" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "orbital part of face", + "xrefs" : [ "FMA:54448" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "orbital region", + "xrefs" : [ "FMA:54448" ] + } ], "xrefs" : [ { - "val" : "RO:0000056" + "val" : "AAO:0010340" + }, { + "val" : "BIRNLEX:1169" + }, { + "val" : "BTO:0004688" + }, { + "val" : "EHDAA2:0000484" + }, { + "val" : "EHDAA:936" + }, { + "val" : "EMAPA:16198" + }, { + "val" : "FMA:54448" + }, { + "val" : "MA:0000261" + }, { + "val" : "NCIT:C12401" + }, { + "val" : "SCTID:181143004" + }, { + "val" : "TAO:0000107" + }, { + "val" : "UMLS:C0015392" + }, { + "val" : "UMLS:C1280202" + }, { + "val" : "VHOG:0000275" + }, { + "val" : "XAO:0000179" + }, { + "val" : "ZFA:0000107" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000020", + "lbl" : "sense organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "An organ that is capable of transducing sensory stimulus to the nervous system.", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/549", "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "organ of sense organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory system organ", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "sensillum", + "xrefs" : [ "WBbt:0006929" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Sinnesorgan", + "xrefs" : [ "BTO:0000202" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "sensor" + } ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "AEO:0000094" + }, { + "val" : "BSA:0000121" + }, { + "val" : "BTO:0000202" + }, { + "val" : "CALOHA:TS-2043" + }, { + "val" : "EHDAA2:0001824" + }, { + "val" : "EHDAA:500" + }, { + "val" : "EMAPA:35955" + }, { + "val" : "FBbt:00005155" + }, { + "val" : "GAID:63" + }, { + "val" : "HAO:0000930" + }, { + "val" : "MA:0000017" + }, { + "val" : "MESH:D012679" + }, { + "val" : "NCIT:C33224" + }, { + "val" : "SCTID:244485009" + }, { + "val" : "UMLS:C0935626" + }, { + "val" : "VHOG:0001407" + }, { + "val" : "WBbt:0006929" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], + "xrefs" : [ { + "val" : "galen:Tube" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000033", + "lbl" : "head", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "The head is the anterior-most division of the body [GO].", + "xrefs" : [ "GO:0060322", "Wikipedia:Head" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "head (volume)", + "xrefs" : [ "FMA:7154" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult head" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cephalic area", + "xrefs" : [ "SPD:0000016" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010335" + }, { + "val" : "AEO:0000106" + }, { + "val" : "BILA:0000115" + }, { + "val" : "BIRNLEX:1230" + }, { + "val" : "BTO:0000282" + }, { + "val" : "CALOHA:TS-0436" + }, { + "val" : "EFO:0000964" + }, { + "val" : "EHDAA2:0003106" + }, { + "val" : "EMAPA:31858" + }, { + "val" : "FMA:7154" + }, { + "val" : "GAID:61" + }, { + "val" : "HAO:0000397" + }, { + "val" : "MA:0000023" + }, { + "val" : "MAT:0000294" + }, { + "val" : "MESH:D006257" + }, { + "val" : "MIAA:0000294" + }, { + "val" : "NCIT:C12419" + }, { + "val" : "SCTID:302548004" + }, { + "val" : "SPD:0000016" + }, { + "val" : "TAO:0001114" + }, { + "val" : "TGMA:0000002" + }, { + "val" : "UMLS:C0018670" + }, { + "val" : "VHOG:0001644" + }, { + "val" : "WBbt:0005739" + }, { + "val" : "Wikipedia:Head" + }, { + "val" : "XAO:0003024" + }, { + "val" : "ZFA:0001114" + }, { + "val" : "galen:Head" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000042", + "lbl" : "serous membrane", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.", + "xrefs" : [ "Wikipedia:Serous_membrane", "https://github.com/obophenotype/uberon/issues/86" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "tunica serosa", + "xrefs" : [ "FMA:9581" ] + }, { + "pred" : "hasExactSynonym", + "val" : "wall of serous sac", + "xrefs" : [ "FMA:9581" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "serosa", + "xrefs" : [ "Wikipedia:Serous_membrane" ] + } ], + "xrefs" : [ { + "val" : "FMA:9581" + }, { + "val" : "GAID:19" + }, { + "val" : "MESH:D012704" + }, { + "val" : "NCIT:C13169" + }, { + "val" : "SCTID:362878009" + }, { + "val" : "TAO:0005425" + }, { + "val" : "UMLS:C0036760" + }, { + "val" : "Wikipedia:Serous_membrane" + }, { + "val" : "ZFA:0005425" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000047", + "lbl" : "simple eye", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.", + "xrefs" : [ "Wikipedia:Eye#Simple_eyes" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "TGMA:0000729" + }, { + "val" : "Wikipedia:Eye#Simple_eyes" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000055", + "lbl" : "vessel", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "A tubular structure that contains, conveys body fluid, such as blood or lymph.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. 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The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.", + "xrefs" : [ "GO:0007369" ] }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blastocystis trilaminaris stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000109" + }, { + "val" : "BilaDO:0000008" + }, { + "val" : "EFO:0001296" + }, { + "val" : "FBdv:00005317" + }, { + "val" : "HsapDv:0000010" + }, { + "val" : "MmusDv:0000013" + }, { + "val" : "OGES:000004" + }, { + "val" : "OGES:000019" + }, { + "val" : "WBls:0000010" + }, { + "val" : "XAO:1000005" + }, { + "val" : "ZFS:0000047" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000110", + "lbl" : "neurula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + "val" : "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.", + "xrefs" : [ "GO:0001841" ] }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BILS:0000110" + }, { + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000122", + "lbl" : "neuron projection bundle", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + "val" : "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.", + "xrefs" : [ "CARO:0001001", "FBC:DOS", "FBbt:00005099" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "funiculus" + }, { + "pred" : "hasExactSynonym", + "val" : "nerve fiber bundle", + "xrefs" : [ "FBbt:00005099" ] + }, { + "pred" : "hasExactSynonym", + "val" : "neural fiber bundle" + } ], + "xrefs" : [ { + "val" : "CARO:0001001" + }, { + "val" : "FBbt:00005099" + }, { + "val" : "NLX:147821" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0005163" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000153", + "lbl" : "anterior region of body", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" - }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000154", + "lbl" : "posterior region of body", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." - }, "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000165", + "lbl" : "mouth", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "xrefs" : [ "Wikipedia:Mouth", "https://github.com/obophenotype/uberon/wiki/The-digestive-tract" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio oralis", + "xrefs" : [ "BTO:0004698", "FMA:49184", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "cavital oralis", + "xrefs" : [ "Wikipedia:Mouth" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavitas oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavum oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth cavity", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral region", + "xrefs" : [ "EHDAA2:0001326" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral vestibule", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "rima oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "stoma" + }, { + "pred" : "hasRelatedSynonym", + "val" : "stomatodaeum", + "xrefs" : [ "VHOG:0000812" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trophic apparatus", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibule of mouth", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibulum oris", + "xrefs" : [ "BTO:0001090" ] + } ], "xrefs" : [ { - "val" : "RO:0002180" + "val" : "AAO:0010355" + }, { + "val" : "BTO:0001090" + }, { + "val" : "BTO:0004698" + }, { + "val" : "CALOHA:TS-1315" + }, { + "val" : "EFO:0000825" + }, { + "val" : "EHDAA2:0001326" + }, { + "val" : "EHDAA:542" + }, { + "val" : "EMAPA:16262" + }, { + "val" : "FBbt:00003126" + }, { + "val" : "FMA:49184" + }, { + "val" : "GAID:75" + }, { + "val" : "MA:0000341" + }, { + "val" : "MA:0002474" + }, { + "val" : "MAT:0000038" + }, { + "val" : "MESH:D009055" + }, { + "val" : "MIAA:0000038" + }, { + "val" : "SCTID:21082005" + }, { + "val" : "TADS:0000040" + }, { + "val" : "TAO:0000547" + }, { + "val" : "TAO:0000590" + }, { + "val" : "TGMA:0000131" + }, { + "val" : "VHOG:0000280" + }, { + "val" : "VHOG:0000812" + }, { + "val" : "Wikipedia:Mouth" + }, { + "val" : "XAO:0003029" + }, { + "val" : "ZFA:0000547" + }, { + "val" : "ZFA:0000590" + }, { + "val" : "galen:Mouth" + }, { + "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "val" : "https://github.com/obophenotype/uberon/issues/661" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "lbl" : "blood", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + "val" : "A fluid that is composed of blood plasma and erythrocytes.", + "xrefs" : [ "FMA:9670", "Wikipedia:Blood", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/9" ] }, - "comments" : [ "TODO - add child relations from DOS" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "portion of blood" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "pred" : "hasExactSynonym", + "val" : "vertebrate blood" + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole blood", + "xrefs" : [ "BTO:0000089" ] + } ], "xrefs" : [ { - "val" : "RO:0002212" + "val" : "AAO:0000046" + }, { + "val" : "BTO:0000089" + }, { + "val" : "CALOHA:TS-0079" + }, { + "val" : "EFO:0000296" + }, { + "val" : "EHDAA2:0000176" + }, { + "val" : "EHDAA:418" + }, { + "val" : "EMAPA:16332" + }, { + "val" : "ENVO:02000027" + }, { + "val" : "EV:0100047" + }, { + "val" : "FMA:9670" + }, { + "val" : "GAID:965" + }, { + "val" : "MA:0000059" + }, { + "val" : "MESH:D001769" + }, { + "val" : "MIAA:0000315" + }, { + "val" : "NCIT:C12434" + }, { + "val" : "TAO:0000007" + }, { + "val" : "UMLS:C0005767" + }, { + "val" : "VHOG:0000224" + }, { + "val" : "Wikipedia:Blood" + }, { + "val" : "XAO:0000124" + }, { + "val" : "ZFA:0000007" + }, { + "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "negatively_regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000179", + "lbl" : "haemolymphatic fluid", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + "val" : "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blood or blood analog" + }, { + "pred" : "hasRelatedSynonym", + "val" : "circulating fluid" + } ], "xrefs" : [ { - "val" : "RO:0002213" + "val" : "CARO:0000081" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "positively_regulates" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-04-08T04:38:19Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", + "lbl" : "blastula", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blastula embryo", + "xrefs" : [ "BILA:0000059" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastosphere", + "xrefs" : [ "Wikipedia:Blastula" ] + } ], "xrefs" : [ { - "val" : "RO:0002215" + "val" : "BILA:0000059" + }, { + "val" : "BTO:0000128" + }, { + "val" : "GAID:1294" + }, { + "val" : "MESH:D036703" + }, { + "val" : "OGEM:000006" + }, { + "val" : "Wikipedia:Blastula" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007011" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002216", - "lbl" : "capable of part of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", + "lbl" : "musculature of body", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." + "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", + "xrefs" : [ "VSAO:0000033" ] }, - "xrefs" : [ { - "val" : "RO:0002216" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "muscle system" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "capable_of_part_of" + "pred" : "hasExactSynonym", + "val" : "muscle system of body" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002219", - "lbl" : "surrounded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002220", - "lbl" : "adjacent to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x adjacent to y if and only if x and y share a boundary." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "pred" : "hasExactSynonym", + "val" : "muscular system", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "musculature system", + "xrefs" : [ "BILA:0000088" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of all muscles", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of muscles of body", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate muscular system", + "xrefs" : [ "BTO:0001369" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "muskelsystem", + "xrefs" : [ "BTO:0001485" ] + } ], "xrefs" : [ { - "val" : "RO:0002220" + "val" : "AAO:0000307" + }, { + "val" : "BILA:0000088" + }, { + "val" : "BTO:0001369" + }, { + "val" : "BTO:0001485" + }, { + "val" : "EFO:0000801" + }, { + "val" : "FMA:72954" + }, { + "val" : "MA:0002888" + }, { + "val" : "MAT:0000025" + }, { + "val" : "MIAA:0000025" + }, { + "val" : "VSAO:0000033" + }, { + "val" : "XAO:0004042" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This relation acts as a join point with BSPO" + "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "adjacent_to" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002221", - "lbl" : "surrounds", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", + "lbl" : "organism substance", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of surrounded by" + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002222", - "lbl" : "temporally related to", - "type" : "PROPERTY", - "meta" : { - "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002223", - "lbl" : "starts", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of starts with" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002224", - "lbl" : "starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "body fluid or substance", + "xrefs" : [ "MA:0002450" ] + }, { + "pred" : "hasExactSynonym", + "val" : "body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organism substance", + "xrefs" : [ "CARO:0000004" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance", + "xrefs" : [ "ZFA:0001487" ] + } ], "xrefs" : [ { - "val" : "RO:0002224" + "val" : "AAO:0010839" + }, { + "val" : "AEO:0000004" + }, { + "val" : "BILA:0000004" + }, { + "val" : "CALOHA:TS-2101" + }, { + "val" : "CARO:0000004" + }, { + "val" : "EHDAA2:0003004" + }, { + "val" : "EMAPA:35178" + }, { + "val" : "FBbt:00007019" + }, { + "val" : "FMA:9669" + }, { + "val" : "HAO:0000004" + }, { + "val" : "MA:0002450" + }, { + "val" : "NCIT:C13236" + }, { + "val" : "SPD:0000008" + }, { + "val" : "TAO:0001487" + }, { + "val" : "TGMA:0001824" + }, { + "val" : "VHOG:0001726" + }, { + "val" : "XAO:0004001" + }, { + "val" : "ZFA:0001487" + }, { + "val" : "galen:BodySubstance" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts_with" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002225", - "lbl" : "develops from part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002226", - "lbl" : "develops in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops_in y if x is located in y whilst x is developing" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002229", - "lbl" : "ends", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of ends with" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002230", - "lbl" : "ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000464", + "lbl" : "anatomical space", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + "val" : "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "lumen" + }, { + "pred" : "hasBroadSynonym", + "val" : "space" + }, { + "pred" : "hasExactSynonym", + "val" : "lumen space" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "anatomical spaces", + "xrefs" : [ "ZFA:0001643" ] + } ], "xrefs" : [ { - 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Consider merging with 'neuron projection bundle'" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "fascicle", + "xrefs" : [ "FBbt:00005101" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "fasciculus" + }, { + "pred" : "hasExactSynonym", + "val" : "nerve bundle", + "xrefs" : [ "FMA:12235" ] + }, { + "pred" : "hasExactSynonym", + "val" : "nerve fasciculus", + "xrefs" : [ "FMA:12235" ] + }, { + "pred" : "hasExactSynonym", + "val" : "neural fasciculus", + "xrefs" : [ "FMA:12235" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "nerve fiber tract", + "xrefs" : [ "BTO:0002191" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:872" + }, { + "val" : "BTO:0002191" + }, { + "val" : "EMAPA:36605" + }, { + "val" : "FMA:12235" + }, { + "val" : "NCIT:C32586" + }, { + "val" : "TGMA:0000088" + }, { + "val" : "UMLS:C1185741" + }, { + "val" : "Wikipedia:Nervous_system_fascicle" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002404", - "lbl" : "causally downstream of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001032", + "lbl" : "sensory system", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of upstream of" + "val" : "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.", + "xrefs" : [ "Wikipedia:Sensory_system" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "organa sensuum", + "xrefs" : [ "FMA:75259", "FMA:TA" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organ subsystem" + }, { + "pred" : "hasExactSynonym", + "val" : "sense organs", + "xrefs" : [ "FMA:75259" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organs set", + "xrefs" : [ "FMA:75259" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory subsystem" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "sensory systems", + "xrefs" : [ "TAO:0000282" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "organa sensuum", + "xrefs" : [ "Wikipedia:Sensory_system" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "sensory organ system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of sense organs", + "xrefs" : [ "FMA:75259" ] + } ], "xrefs" : [ { - "val" : "RO:0002404" + "val" : "AAO:0000555" + }, { + "val" : "BAMS:SEN" + }, { + "val" : "BILA:0000099" + }, { + "val" : "EFO:0000805" + }, { + "val" : "EHDAA2:0003094" + }, { + "val" : "EMAPA:16192" + }, { + "val" : "FBbt:00007692" + }, { + "val" : "FMA:75259" + }, { + "val" : "MA:0002442" + }, { + "val" : "MAT:0000031" + }, { + "val" : "MIAA:0000031" + }, { + "val" : "NLXANAT:090816" + }, { + "val" : "TAO:0000282" + }, { + "val" : "VHOG:0001674" + }, { + "val" : "Wikipedia:Sensory_system" + }, { + "val" : "XAO:0003194" + }, { + "val" : "ZFA:0000282" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_downstream_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002410", - "lbl" : "causally related to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", - "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This branch of the ontology deals with causal relations between entities. 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001048", + "lbl" : "primordium", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + "val" : "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. 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The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].", + "xrefs" : [ "Wikipedia:Neural_tube" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "affects" + "val" : "neural primordium" + }, { + "pred" : "hasRelatedSynonym", + "val" : "presumptive central nervous system" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tubus neuralis", + "xrefs" : [ "Wikipedia:Neural_tube" ] } ], "xrefs" : [ { - "val" : "RO:0002418" + "val" : "AAO:0010617" + }, { + "val" : "BTO:0001057" + }, { + "val" : "CALOHA:TS-2371" + }, { + "val" : "DHBA:10154" + }, { + "val" : "EHDAA2:0001254" + }, { + "val" : "EHDAA:2869" + }, { + "val" : "EHDAA:908" + }, { + "val" : "EMAPA:16164" + }, { + "val" : "EMAPA:16757" + }, { + "val" : "FMA:293882" + }, { + "val" : "MAT:0000069" + }, { + "val" : "MIAA:0000069" + }, { + "val" : "NCIT:C34226" + }, { + "val" : "SCTID:362852000" + }, { + "val" : "TAO:0001135" + }, { + "val" : "UMLS:C0231024" + }, { + "val" : "VHOG:0000307" + }, { + "val" : "Wikipedia:Neural_tube" + }, { + "val" : "XAO:0003204" + }, { + "val" : "ZFA:0001135" + }, { + "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_upstream_of_or_within" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002427", - "lbl" : "causally downstream of or within", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001062", + "lbl" : "anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "inverse of causally upstream of or within" + "val" : "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.", + "xrefs" : [ "FMA:62955", "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002427" + "val" : "AAO:0010841" + }, { + "val" : "AEO:0000000" + }, { + "val" : "BFO:0000004" + }, { + "val" : "BILA:0000000" + }, { + "val" : "BIRNLEX:6" + }, { + "val" : "CARO:0000000" + }, { + "val" : "EHDAA2:0002229" + }, { + "val" : "FBbt:10000000" + }, { + "val" : "FMA:62955" + }, { + "val" : "HAO:0000000" + }, { + "val" : "MA:0000001" + }, { + "val" : "NCIT:C12219" + }, { + "val" : "TAO:0100000" + }, { + "val" : "TGMA:0001822" + }, { + "val" : "UMLS:C1515976" + }, { + "val" : "WBbt:0000100" + }, { + "val" : "XAO:0000000" + }, { + "val" : "ZFA:0100000" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "causally_downstream_of_or_within" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002428", - "lbl" : "involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002431", - "lbl" : "involved in or involved in regulation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "OWL does not allow defining object properties via a Union" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002433", - "lbl" : "contributes to morphology of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", - "lbl" : "composed primarily of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", - "lbl" : "has part that occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "lbl" : "receives input from", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "lbl" : "sends output to", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", - "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", - "lbl" : "existence starts during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. 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The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "exists during" + "val" : "involuntary muscle" + }, { + "pred" : "hasExactSynonym", + "val" : "non-striated muscle" + }, { + "pred" : "hasExactSynonym", + "val" : "smooth muscle" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "textus muscularis nonstriatus", + "xrefs" : [ "FMA:14070", "FMA:TA" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasNarrowSynonym", + "val" : "visceral muscle" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasNarrowSynonym", + "val" : "visceral muscle tissue" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "textus muscularis levis; textus muscularis nonstriatus", + "xrefs" : [ "Wikipedia:Smooth_muscle_tissue" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010244" + }, { + "val" : "AEO:0000141" + }, { + "val" : "BTO:0001260" + }, { + "val" : "CALOHA:TS-0943" + }, { + "val" : "EFO:0000889" + }, { + "val" : "EHDAA2:0003141" + }, { + "val" : "EMAPA:32717" + }, { + "val" : "EV:0100378" + }, { + "val" : "FMA:14070" + }, { + "val" : "GAID:167" + }, { + "val" : "MA:0000166" + }, { + "val" : "MAT:0000303" + }, { + "val" : "MESH:D009130" + }, { + "val" : "MIAA:0000303" + }, { + "val" : "NCIT:C12437" + }, { + "val" : "TAO:0005274" + }, { + "val" : "UMLS:C1267092" + }, { + "val" : "VHOG:0001246" + }, { + "val" : "WBbt:0005781" + }, { + "val" : "Wikipedia:Smooth_muscle_tissue" + }, { + "val" : "XAO:0000175" + }, { + "val" : "ZFA:0005274" + }, { + "val" : "galen:SmoothMuscle" + }, { + "val" : "galen:SmoothMuscleTissue" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", - "lbl" : "existence ends during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. 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The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].", + "xrefs" : [ "FMA:62004", "GO:0021550", "Wikipedia:Bone_marrow_of_ovary_oblongata" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of blood" + "pred" : "hasBroadSynonym", + "val" : "bulb" + }, { + "pred" : "hasBroadSynonym", + "val" : "medulla", + "xrefs" : [ "ABA:MY" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "vertebrate blood" + "val" : "bulbus", + "xrefs" : [ "FMA:62004", "FMA:TA" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "whole blood", - "xrefs" : [ "BTO:0000089" ] + "val" : "medulla oblonzata", + "xrefs" : [ "Wikipedia:Medulla_oblongata" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metepencephalon", + "xrefs" : [ "FMA:62004" ] } ], "xrefs" : [ { - "val" : "AAO:0000046" + "val" : "AAO:0010486" }, { - "val" : "BTO:0000089" + "val" : "BAMS:MY" }, { - "val" : "CALOHA:TS-0079" + "val" : "BAMS:Md" }, { - "val" : "EFO:0000296" + "val" : "BIRNLEX:957" }, { - "val" : "EHDAA2:0000176" + "val" : "BM:Me" }, { - "val" : "EHDAA:418" + "val" : "BTO:0000041" }, { - "val" : "EMAPA:16332" + "val" : "CALOHA:TS-0607" }, { - "val" : "ENVO:02000027" + "val" : "DMBA:17352" }, { - "val" : "EV:0100047" + "val" : "EFO:0000924" }, { - "val" : "FMA:9670" + "val" : "EHDAA2:0001088" }, { - "val" : "GAID:965" + "val" : "EHDAA:7588" }, { - "val" : "MA:0000059" + "val" : "EMAPA:17550" }, { - "val" : "MESH:D001769" + "val" : "EV:0100275" }, { - "val" : "MIAA:0000315" + "val" : "FMA:62004" }, { - "val" : "NCIT:C12434" + "val" : "GAID:590" }, { - "val" : "TAO:0000007" + "val" : "MA:0000206" }, { - "val" : "UMLS:C0005767" + "val" : "MAT:0000111" }, { - "val" : "VHOG:0000224" + "val" : "MAT:0000367" }, { - "val" : "Wikipedia:Blood" + "val" : "MBA:354" }, { - "val" : "XAO:0000124" + "val" : "MESH:D008526" }, { - "val" : "ZFA:0000007" + "val" : "MIAA:0000111" }, { - "val" : "galen:Blood" + "val" : "NCIT:C12442" + }, { + "val" : "SCTID:279104005" + }, { + "val" : "TAO:0000545" + }, { + "val" : "UMLS:C0025148" + }, { + "val" : "UMLS:C1269575" + }, { + "val" : "VHOG:0000181" + }, { + "val" : "Wikipedia:Bone_marrow_of_ovary_oblongata" + }, { + "val" : "XAO:0003100" + }, { + "val" : "ZFA:0000545" + }, { + "val" : "neuronames:698" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -17594,3235 +20575,3334 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "lbl" : "haemolymphatic fluid", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001908", + "lbl" : "optic tract", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF].", + "xrefs" : [ "NIFSTD", "Wikipedia:Optic_tract", "ZFIN:curator" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "blood or blood analog" + "pred" : "hasExactSynonym", + "val" : "optic lemniscus" }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "circulating fluid" - } ], - "xrefs" : [ { - "val" : "CARO:0000081" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-6601-2165" + "val" : "optic tracts", + "xrefs" : [ "ZFA:0000252" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2009-04-08T04:38:19Z" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tractus optici", + "xrefs" : [ "NeuroNames:460" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", - "lbl" : "blastula", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", - "xrefs" : [ "Wikipedia:Blastula" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blastula embryo", - "xrefs" : [ "BILA:0000059" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tractus opticus", + "xrefs" : [ "Wikipedia:Optic_tract" ] }, { "pred" : "hasRelatedSynonym", - "val" : "blastosphere", - "xrefs" : [ "Wikipedia:Blastula" ] + "val" : "visual pathway", + "xrefs" : [ "GAID:735" ] } ], "xrefs" : [ { - "val" : "BILA:0000059" + "val" : "BAMS:opt" }, { - "val" : "BTO:0000128" + "val" : "BIRNLEX:1684" }, { - "val" : "GAID:1294" + "val" : "BM:Tel-OT" }, { - "val" : "MESH:D036703" + "val" : "DHBA:10589" }, { - "val" : "OGEM:000006" + "val" : "DMBA:17785" }, { - "val" : "Wikipedia:Blastula" + "val" : "EMAPA:35617" + }, { + "val" : "FMA:62046" + }, { + "val" : "GAID:735" + }, { + "val" : "HBA:9309" + }, { + "val" : "MA:0001099" + }, { + "val" : "MBA:125" + }, { + "val" : "MESH:D014795" + }, { + "val" : "NCIT:C33218" + }, { + "val" : "SCTID:280952003" + }, { + "val" : "TAO:0000252" + }, { + "val" : "UMLS:C0152405" + }, { + "val" : "VHOG:0001164" + }, { + "val" : "Wikipedia:Optic_tract" + }, { + "val" : "XAO:0004101" + }, { + "val" : "ZFA:0000252" + }, { + "val" : "neuronames:460" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" + "val" : "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "lbl" : "musculature of body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001943", + "lbl" : "midbrain tegmentum", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", - "xrefs" : [ "VSAO:0000033" ] + "val" : "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].", + "xrefs" : [ "FMA:FMA", "ISBN:0471888893", "Wikipedia:Midbrain_tegmentum" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "muscle system" - }, { - "pred" : "hasExactSynonym", - "val" : "muscle system of body" - }, { - "pred" : "hasExactSynonym", - "val" : "muscular system", - "xrefs" : [ "FMA:72954" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasBroadSynonym", + "val" : "MTg", + "xrefs" : [ "BIRNLEX:1200", "NIFSTD:NeuroNames_abbrevSource" ] }, { - "pred" : "hasExactSynonym", - "val" : "musculature system", - "xrefs" : [ "BILA:0000088" ] + "pred" : "hasBroadSynonym", + "val" : "tegmentum", + "xrefs" : [ "ISBN:0471888893" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "set of all muscles", - "xrefs" : [ "FMA:72954" ] + "val" : "tegmentum mesencephali", + "xrefs" : [ "Wikipedia:Midbrain_tegmentum" ] }, { "pred" : "hasExactSynonym", - "val" : "set of muscles of body", - "xrefs" : [ "FMA:72954" ] + "val" : "tegmentum of midbrain" }, { - "pred" : "hasExactSynonym", - "val" : "vertebrate muscular system", - "xrefs" : [ "BTO:0001369" ] + "pred" : "hasRelatedSynonym", + "val" : "mesencephalic tegmentum", + "xrefs" : [ "VHOG:0001367" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "muskelsystem", - "xrefs" : [ "BTO:0001485" ] + "val" : "tegmentum mesencephalicum", + "xrefs" : [ "NeuroNames:491" ] } ], "xrefs" : [ { - "val" : "AAO:0000307" + "val" : "BAMS:MTg" }, { - "val" : "BILA:0000088" + "val" : "BIRNLEX:1200" }, { - "val" : "BTO:0001369" + "val" : "BTO:0003388" }, { - "val" : "BTO:0001485" + "val" : "DHBA:12195" + }, { + "val" : "EFO:0000921" + }, { + "val" : "EHDAA2:0004475" + }, { + "val" : "EMAPA:18215" + }, { + "val" : "FMA:62393" + }, { + "val" : "HBA:9002" + }, { + "val" : "MA:0000212" + }, { + "val" : "MAT:0000452" + }, { + "val" : "SCTID:362392007" }, { - "val" : "EFO:0000801" + "val" : "TAO:0000160" }, { - "val" : "FMA:72954" + "val" : "UMLS:C0039441" }, { - "val" : "MA:0002888" + "val" : "VHOG:0001367" }, { - "val" : "MAT:0000025" + "val" : "Wikipedia:Midbrain_tegmentum" }, { - "val" : "MIAA:0000025" + "val" : "XAO:0004271" }, { - "val" : "VSAO:0000033" + "val" : "ZFA:0000160" }, { - "val" : "XAO:0004042" + "val" : "neuronames:491" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "lbl" : "blood plasma", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "The liquid component of blood, in which erythrocytes are suspended.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "body fluid or substance", - "xrefs" : [ "MA:0002450" ] - }, { - "pred" : "hasExactSynonym", - "val" : "body substance", - "xrefs" : [ "FMA:9669" ] + "pred" : "hasBroadSynonym", + "val" : "plasma", + "xrefs" : [ "MA:0002501" ] }, { - "pred" : "hasExactSynonym", - "val" : "organism substance", - "xrefs" : [ "CARO:0000004" ] + "pred" : "hasBroadSynonym", + "val" : "portion of plasma", + "xrefs" : [ "FMA:62970" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of body substance", - "xrefs" : [ "FMA:9669" ] + "val" : "blood plasm" }, { "pred" : "hasExactSynonym", - "val" : "portion of organism substance", - "xrefs" : [ "ZFA:0001487" ] + "val" : "portion of blood plasma" } ], "xrefs" : [ { - "val" : "AAO:0010839" - }, { - "val" : "AEO:0000004" - }, { - "val" : "BILA:0000004" - }, { - "val" : "CALOHA:TS-2101" - }, { - "val" : "CARO:0000004" - }, { - "val" : "EHDAA2:0003004" - }, { - "val" : "EMAPA:35178" + "val" : "BTO:0000131" }, { - "val" : "FBbt:00007019" + "val" : "CALOHA:TS-0800" }, { - "val" : "FMA:9669" + "val" : "EFO:0001905" }, { - "val" : "HAO:0000004" + "val" : "EMAPA:35690" }, { - "val" : "MA:0002450" + "val" : "FMA:62970" }, { - "val" : "NCIT:C13236" + "val" : "GAID:1178" }, { - "val" : "SPD:0000008" + "val" : "MA:0002501" }, { - "val" : "TAO:0001487" + "val" : "MAT:0000052" }, { - "val" : "TGMA:0001824" + "val" : "MESH:D010949" }, { - "val" : "VHOG:0001726" + "val" : "MIAA:0000052" }, { - "val" : "XAO:0004001" + "val" : "NCIT:C13356" }, { - 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it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.", + "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "visceral organ", + "xrefs" : [ "RETIRED_EHDAA2:0002201" ] + }, { + "pred" : "hasExactSynonym", + "val" : "visceral organ system", + "xrefs" : [ "MA:0000019" ] + }, { "pred" : "hasRelatedSynonym", - "val" : "acellular anatomical structures", - "xrefs" : [ "ZFA:0000382" ] + "val" : "splanchnic tissue", + "xrefs" : [ "BTO:0001491" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "viscera" + }, { + "pred" : "hasRelatedSynonym", + "val" : "visceral tissue", + "xrefs" : [ "BTO:0001491" ] } ], "xrefs" : [ { - "val" : "AAO:0010268" + "val" : "AAO:0010386" }, { - "val" : "AEO:0000040" + "val" : "BTO:0001491" }, { - "val" : "BILA:0000040" + "val" : "EHDAA:512" }, { - "val" : "CARO:0000040" + "val" : "EMAPA:16245" }, { - "val" : "EHDAA2:0003040" + "val" : "FMA:7085" }, { - "val" : "FBbt:00007013" + "val" : "MA:0000019" }, { - "val" : "FMA:63863" + "val" : "MESH:D014781" }, { - "val" : "HAO:0000040" + "val" : "NCIT:C28287" }, { - "val" : "TAO:0000382" + "val" : "RETIRED_EHDAA2:0002201" }, { - "val" : "TGMA:0001841" + "val" : "SCTID:118760003" }, { - "val" : "XAO:0003162" + "val" : "UMLS:C0042779" }, { - "val" : "ZFA:0000382" + "val" : "Wikipedia:Viscus" + }, { + "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", - "lbl" : "anatomical cluster", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", + "lbl" : "postcranial axial skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical group whose component anatomical structures lie in close proximity to each other.", - "xrefs" : [ "FBbt:00007277" ] + "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", + "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FBbt:00007277" + "comments" : [ "previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "axial skeleton", + "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] }, { - "val" : "VHOG:0001737" + "pred" : "hasExactSynonym", + "val" : "post-cranial axial skeleton" } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + "xrefs" : [ { + "val" : "AAO:0000034" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "val" : "EFO:0000942" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "EHDAA2:0000161" + }, { + "val" : "EHDAA:5049" + }, { + "val" : "EMAPA:37721" + }, { + "val" : "FMA:71221" + }, { + "val" : "MA:0002986" + }, { + "val" : "MAT:0000148" + }, { + "val" : "MIAA:0000148" + }, { + "val" : "TAO:0000317" + }, { + "val" : "VHOG:0000317" + }, { + "val" : "VSAO:0000093" + }, { + "val" : "XAO:0003073" }, { + "val" : "ZFA:0000317" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", - "lbl" : "tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", + "lbl" : "trunk", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", - "xrefs" : [ "CARO:0000043" ] + "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. 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Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "embryonic tissue", - "xrefs" : [ "FMA:69069" ] + "pred" : "hasExactSynonym", + "val" : "CNS tract/commissure", + "xrefs" : [ "ZFA:0001682" ] }, { "pred" : "hasExactSynonym", - "val" : "germinal layer", - "xrefs" : [ "ncithesaurus:Germinal_Layer" ] + "val" : "neuronal white matter", + "xrefs" : [ "AEO:0001011" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "primary germ layer", - "xrefs" : [ "GO:0001704", "ZFA:0001122" ] + "pred" : "hasExactSynonym", + "val" : "white matter of neuraxis", + "xrefs" : [ "FMA:83929" ] + }, { + "pred" : "hasExactSynonym", + "val" : "white substance" }, { "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layer" + "val" : "CNS tracts and commissures", + "xrefs" : [ "TAO:0000145" ] }, { "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layers" + "val" : "CNS white matter", + "xrefs" : [ "TAO:0002143" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "substantia alba", + "xrefs" : [ "Wikipedia:White_matter" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "white mater", + "xrefs" : [ "VHOG:0001764" ] } ], "xrefs" : [ { - "val" : "AAO:0000480" + "val" : "AEO:0000139" }, { - "val" : "BILA:0000035" + "val" : "AEO:0001011" }, { - "val" : "BTO:0000556" + "val" : "EMAPA:35927" }, { - "val" : "EMAPA:36033" + "val" : "FMA:83929" }, { - "val" : "FBbt:00000110" + "val" : "HBA:9218" }, { - "val" : "FMA:69069" + "val" : "MA:0001135" }, { - "val" : "GAID:1303" + "val" : "NCIT:C33892" }, { - "val" : "MESH:D005855" + "val" : "NLX:412" }, { - "val" : "NCIT:C12950" + "val" : "NLXANAT:101177" }, { - "val" : "NCIT:C54105" + "val" : "PBA:294022044" }, { - "val" : "TAO:0001122" + "val" : "TAO:0000145" }, { - "val" : "UMLS:C0920502" + "val" : "TAO:0002142" }, { - "val" : "UMLS:C1708239" + "val" : "TAO:0002143" }, { - "val" : "VHOG:0001223" + "val" : "UMLS:C0682708" }, { - "val" : "Wikipedia:Germ_layer" + "val" : "VHOG:0001764" }, { - "val" : "XAO:0003011" + "val" : "Wikipedia:White_matter" }, { - "val" : "ZFA:0001122" + "val" : "ZFA:0001682" + }, { + "val" : "neuronames:2870" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", - "lbl" : "ectoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", + "lbl" : "coelemic cavity lumen", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", - "xrefs" : [ "Wikipedia:Ectoderm" ] + "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. 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In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "pred" : "hasExactSynonym", + "val" : "embryonic notocord" + }, { + "pred" : "hasExactSynonym", + "val" : "notocord", + "xrefs" : [ "ZFA:0000135" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "entoderm", - "xrefs" : [ "DOI:10.5962/bhl.title.1013" ] + "val" : "notochorda", + "xrefs" : [ "Wikipedia:Notochord" ] } ], "xrefs" : [ { - "val" : "AAO:0000139" + "val" : "AAO:0000327" }, { - "val" : "BILA:0000038" + "val" : "BTO:0001768" }, { - "val" : "BTO:0000800" + "val" : "CALOHA:TS-0690" }, { - "val" : "CALOHA:TS-0273" + "val" : "EHDAA2:0001277" }, { - "val" : "EFO:0002545" + "val" : "EHDAA:1241" }, { - "val" : "EHDAA2:0000436" + "val" : "EHDAA:6021" }, { - "val" : "EMAPA:16062" + "val" : "EMAPA:16191" }, { - "val" : "EV:0100005" + "val" : "EV:0100002" }, { - "val" : "FBbt:00000125" + "val" : "FMA:85521" }, { - "val" : "FMA:69071" + "val" : "GAID:1311" }, { - "val" : "GAID:1305" + "val" : "MAT:0000281" }, { - "val" : "MAT:0000175" + "val" : "MESH:D009672" }, { - "val" : "MESH:D004707" + "val" : "NCIT:C12463" }, { - "val" : "MIAA:0000175" + "val" : "SCTID:308820002" }, { - "val" : "NCIT:C12706" + "val" : "TAO:0000135" }, { - "val" : "SCTID:362855003" + "val" : "UMLS:C0028439" }, { - "val" : "TAO:0000017" + "val" : "VHOG:0000199" }, { - "val" : "UMLS:C0014144" + "val" : "VSAO:0000032" }, { - "val" : "VHOG:0000154" + "val" : "Wikipedia:Notochord" }, { - "val" : "Wikipedia:Endoderm" + "val" : "XAO:0000055" }, { - "val" : "XAO:0000090" + "val" : "ZFA:0000135" }, { - "val" : "ZFA:0000017" + "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "lbl" : "mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002329", + "lbl" : "somite", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The middle germ layer of the embryo, between the endoderm and ectoderm.", - "xrefs" : [ "Wikipedia:Mesoderm" ] + "val" : "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.", + "xrefs" : [ "DOI:10.1111/j.1439-0426.2012.01987.x", "Wikipedia:Somite" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "embryonic mesoderm", - "xrefs" : [ "VHOG:0000152" ] + "pred" : "hasBroadSynonym", + "val" : "mesodermal cluster", + "xrefs" : [ "GO:0001756" ] }, { "pred" : "hasRelatedSynonym", - "val" : "entire mesoderm", - "xrefs" : [ "SCTID:362854004", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "epimere", + "xrefs" : [ "ISBN:0073040584" ] }, { "pred" : "hasRelatedSynonym", - "val" : "mesodermal mantle" - } ], - "xrefs" : [ { - "val" : "AAO:0000304" - }, { - "val" : "BILA:0000037" - }, { - "val" : "BTO:0000839" + "val" : "epimere mesoderm" }, { - "val" : "CALOHA:TS-0623" + "pred" : "hasRelatedSynonym", + "val" : "epithelial somite", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] }, { - "val" : "EFO:0001981" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "somites" }, { - "val" : "EHDAA2:0001128" + "pred" : "hasRelatedSynonym", + "val" : "somitic mesoderm" }, { - "val" : "EHDAA:124" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "somitus", + "xrefs" : [ "Wikipedia:Somite" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010569" }, { - "val" : "EHDAA:160" + "val" : "AEO:0001015" }, { - "val" : "EHDAA:183" + "val" : "BTO:0001558" }, { - "val" : "EMAPA:16083" + "val" : "EHDAA2:0003436" }, { - "val" : "EV:0100006" + "val" : "EHDAA:366" }, { - "val" : "FBbt:00000126" + "val" : "EHDAA:699" }, { - "val" : "FMA:69072" + "val" : "EMAPA:31169" }, { - "val" : "GAID:522" + "val" : "FMA:85522" }, { - "val" : "MAT:0000174" + "val" : "GAID:1306" }, { - "val" : "MESH:D008648" + "val" : "MAT:0000068" }, { - "val" : "MIAA:0000174" + "val" : "MESH:D019170" }, { - "val" : "NCIT:C12750" + "val" : "MIAA:0000068" }, { - "val" : "SCTID:362854004" + "val" : "NCIT:C34302" }, { - "val" : "TAO:0000041" + "val" : "TAO:0000155" }, { - "val" : "UMLS:C0025485" + "val" : "UMLS:C0376449" }, { - "val" : "VHOG:0000152" + "val" : "VHOG:0000191" }, { - "val" : "Wikipedia:Mesoderm" + "val" : "Wikipedia:Somite" }, { - "val" : "XAO:0000050" + "val" : "XAO:0000058" }, { - "val" : "ZFA:0000041" + "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "lbl" : "stomodeum", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "lbl" : "neural crest", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anterior part of the embryonic digestive tract that develops into a mouth. 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In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasExactSynonym", + "val" : "muscular tissue" }, { - "val" : "GAID:174" + "pred" : "hasExactSynonym", + "val" : "portion of muscle tissue", + "xrefs" : [ "FMA:9641" ] }, { - "val" : "MA:0000072" + "pred" : "hasExactSynonym", + "val" : "textus muscularis" + } ], + "xrefs" : [ { + "val" : "AAO:0000306" }, { - "val" : "MAT:0000036" + "val" : "AEO:0000122" }, { - "val" : "MESH:D006321" + "val" : "CALOHA:TS-0642" }, { - "val" : "MIAA:0000036" + "val" : "EHDAA2:0003122" }, { - "val" : "NCIT:C12727" + "val" : "EMAPA:32715" }, { - "val" : "SCTID:302509004" + "val" : "FMA:9641" }, { - "val" : "TAO:0000114" + "val" : "MA:0002437" }, { - "val" : "UMLS:C0018787" + "val" : "MESH:D009132" }, { - "val" : "VHOG:0000276" + "val" : "NCIT:C12435" }, { - "val" : "Wikipedia:Heart" + "val" : "SCTID:91727004" }, { - "val" : "XAO:0000064" + "val" : "UMLS:C2328219" }, { - "val" : "ZFA:0000114" + "val" : "Wikipedia:Muscle_tissue" }, { - "val" : "galen:Heart" + "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6239" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000955", - "lbl" : "brain", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", + "lbl" : "hematopoietic system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. 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"val" : "SCTID:258335003" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002506", + "lbl" : "iris epithelium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelium that is part of a iris [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "epithelial tissue of iris", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "TAO:0000008" + "pred" : "hasExactSynonym", + "val" : "epithelium of iris", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "UMLS:C0006104" + "pred" : "hasExactSynonym", + "val" : "epithelium pigmentosum (iris)", + "xrefs" : [ "FMA:58517" ] }, { - "val" : "UMLS:C1269537" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "epithelium pigmentosum iridis", + "xrefs" : [ "FMA:58517", "FMA:TA" ] }, { - 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}, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000957", - "lbl" : "lamina", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", + "lbl" : "epiblast (generic)", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any thin layer or plate.", - "xrefs" : [ "Wikipedia:Lamina_of_the_vertebral_arch" ] + "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", + "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "laminar tissue" + "val" : "epiblast", + "xrefs" : [ "VHOG:0000243" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastocyst" + }, { + "pred" : "hasRelatedSynonym", + "val" : "ectoblast", + "xrefs" : [ "MP:0003886" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "epiblastus", + "xrefs" : [ "Wikipedia:Epiblast" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "primitive ectoderm", + "xrefs" : [ "VHOG:0000243" ] } ], "xrefs" : [ { - "val" : "Wikipedia:Lamina_of_the_vertebral_arch" + "val" : "BTO:0004593" + }, { + "val" : "FMA:296704" + }, { + "val" : "MAT:0000067" + }, { + "val" : "MIAA:0000067" + }, { + "val" : "VHOG:0000243" + }, { + "val" : "Wikipedia:Epiblast" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - merge with cell layer?" + "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. 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With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.", + "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK53175/", "https://github.com/obophenotype/uberon/issues/135", "https://github.com/seger/aao/issues/4", "https://orcid.org/0000-0002-6601-2165", "https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "chiasma opticum", - "xrefs" : [ "Wikipedia:Optic_chiasm" ] + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "pred" : "hasBroadSynonym", + "val" : "ectodermal placode", + "xrefs" : [ "FMA:293966", "PMID:22512454" ] }, { - "pred" : "hasExactSynonym", - "val" : "decussation of optic nerve fibers", - "xrefs" : [ "FMA:62045" ] + "pred" : "hasBroadSynonym", + "val" : "placode", + "xrefs" : [ "Wikipedia:Placode" ] }, { "pred" : "hasExactSynonym", - "val" : "optic chiasm", - "xrefs" : [ "Wikipedia:Optic_chiasm" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "chiasma", - "xrefs" : [ "NeuroNames:459" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "chiasma nervorum opticorum", - "xrefs" : [ "NeuroNames:459" ] + "val" : "ectodermal cranial placode", + "xrefs" : [ "UBERON:cjm" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "optic chiasm (Rufus of Ephesus)", - "xrefs" : [ "NeuroNames:459" ] + "val" : "cranial placodes", + "xrefs" : [ "XAO:0000305" ] } ], "xrefs" : [ { - "val" : "AAO:0010622" - }, { - "val" : "BAMS:DC" - }, { - "val" : "BAMS:OC" - }, { - "val" : "BAMS:och" - }, { - "val" : "BAMS:ox" - }, { - "val" : "BIRNLEX:1416" + "val" : "AAO:0010466" }, { - "val" : "BM:Tel-OCX" + "val" : "EFO:0001650" }, { - "val" : "DHBA:10644" + "val" : "MAT:0000369" }, { - "val" : "DMBA:17783" + "val" : "MIAA:0000369" }, { - "val" : "EHDAA2:0001302" + "val" : "XAO:0000305" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Do not merge with neurogenic placode" }, { - "val" : "EHDAA:10227" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", + "lbl" : "anatomical cavity", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", + "xrefs" : [ "FMA:67552" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cavity" + } ], + "xrefs" : [ { + "val" : "BIRNLEX:1011" }, { - "val" : "EMAPA:17603" + "val" : "EMAPA:37442" }, { - "val" : "FMA:62045" + "val" : "FMA:67552" }, { - "val" : "GAID:832" + "val" : "MA:0002447" }, { - "val" : "HBA:9310" + "val" : "NCIT:C34007" }, { - "val" : "MA:0001098" + "val" : "galen:Cavity" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0002616", + "lbl" : "regional part of brain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. 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Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", + "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] }, - "comments" : [ "Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. 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Contrast with parenchyma.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "facia/facies", - "xrefs" : [ "Wikipedia:Face" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "visage", - "xrefs" : [ "BTO:0003369" ] + "val" : "stromal connective tissue" } ], "xrefs" : [ { - "val" : "BTO:0003369" - }, { - "val" : "CALOHA:TS-2216" - }, { - "val" : "EMAPA:32763" - }, { - "val" : "FMA:24728" - }, { - "val" : "GAID:64" - }, { - "val" : "HAO:0000316" - }, { - "val" : "MA:0002473" - }, { - "val" : "MESH:D005145" - }, { - "val" : "NCIT:C13071" - }, { - "val" : "SCTID:302549007" - }, { - "val" : "UMLS:C0015450" + "val" : "FMA:81494" }, { - "val" : "Wikipedia:Face" + "val" : "NCIT:C67387" }, { - "val" : "galen:Face" + "val" : "UMLS:C0927195" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "lbl" : "digestive tract", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003902", + "lbl" : "retinal neural layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A tube extending from the mouth to the anus.", - "xrefs" : [ "Wikipedia:Talk:Human_gastrointestinal_tract", "https://github.com/geneontology/go-ontology/issues/7549" ] + "val" : "The part of the retina that contains neurons and photoreceptor cells[GO].", + "xrefs" : [ "GO:0003407" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "gut" - }, { "pred" : "hasExactSynonym", - "val" : "digestive tube" + "val" : "neural layer of retina", + "xrefs" : [ "FMA:58628" ] }, { "pred" : "hasExactSynonym", - "val" : "enteric tract", - "xrefs" : [ "ZFA:0000112" ] + "val" : "neural retina", + "xrefs" : [ "XAO:0003216", "ZFA:0000046" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary canal" + "pred" : "hasExactSynonym", + "val" : "neuroretina", + "xrefs" : [ "ZFA:0000046" ] }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary tract" + "pred" : "hasExactSynonym", + "val" : "stratum nervosum (retina)", + "xrefs" : [ "FMA:58628" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "digestive canal", - "xrefs" : [ "BTO:0000058" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "stratum nervosum retinae", + "xrefs" : [ "FMA:58628", "FMA:TA" ] }, { "pred" : "hasRelatedSynonym", - "val" : "gut tube" + "val" : "neural retinal epithelium", + "xrefs" : [ "MA:000027" ] } ], "xrefs" : [ { - "val" : "AAO:0010023" - }, { - "val" : "BILA:0000083" - }, { - "val" : "BTO:0000511" - }, { - "val" : "BTO:0000545" + "val" : "AAO:0011095" }, { - "val" : "EHDAA2:0000726" + "val" : "BTO:0000929" }, { - "val" : "EHDAA:518" + "val" : "CALOHA:TS-0685" }, { - "val" : "EMAPA:16247" + "val" : "EHDAA2:0001253" }, { - "val" : "FBbt:00003125" + "val" : "EHDAA:4763" }, { - "val" : "FMA:45615" + "val" : "EMAPA:17171" }, { - "val" : "MA:0000917" + "val" : "EMAPA:18590" }, { - "val" : "NCIT:C34082" + "val" : "FMA:58628" }, { - "val" : "TAO:0000112" + "val" : "MA:0000277" }, { - "val" : "TGMA:0001819" + "val" : "NCIT:C33166" }, { - "val" : "UMLS:C0017189" + "val" : "TAO:0000046" }, { - "val" : "VHOG:0000309" + "val" : "UMLS:C1518263" }, { - "val" : "WBbt:0005743" + "val" : "VHOG:0000535" }, { - "val" : "ZFA:0000112" + "val" : "XAO:0003216" }, { - "val" : "galen:AlimentaryTract" + "val" : "ZFA:0000046" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_41324" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -21394,98 +24561,97 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001605", - "lbl" : "ciliary muscle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", + "lbl" : "epithelial tube", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].", - "xrefs" : [ "Wikipedia:Ciliary_muscle" ] + "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", + "xrefs" : [ "GO:0060562", "PMID:12526790" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "musculus ciliarus", - "xrefs" : [ "BTO:0000654" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bowman`s muscles", - "xrefs" : [ "BTO:0000654" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ciliaris", - "xrefs" : [ "Wikipedia:Ciliary_muscle" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "musculus ciliaris", - "xrefs" : [ "Wikipedia:Ciliary_muscle" ] + "val" : "epithelial or endothelial tube" } ], "xrefs" : [ { - "val" : "BTO:0000654" - }, { - "val" : "EMAPA:35240" - }, { - "val" : "FMA:49151" - }, { - "val" : "MA:0001269" - }, { - "val" : "NCIT:C32315" - }, { - "val" : "SCTID:280862009" + "val" : "AEO:0000114" }, { - "val" : "UMLS:C0559230" + "val" : "EHDAA2:0003114" }, { - "val" : "Wikipedia:Ciliary_muscle" + "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001630", - "lbl" : "muscle organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003931", + "lbl" : "diencephalic white matter", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].", - "xrefs" : [ "GO:0007517" ] + "val" : "White matter that is part of a diencephalon [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "muscle", - "xrefs" : [ "ZFA:0005145" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37474" - }, { - "val" : "EV:0100146" + "pred" : "hasExactSynonym", + "val" : "diencephalic tract/commissure", + "xrefs" : [ "ZFA:0000338" ] }, { - "val" : "FMA:5022" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasExactSynonym", + "val" : "diencephalic tracts and commissures", + "xrefs" : [ "TAO:0000338" ] }, { - "val" : "GAID:131" + "pred" : "hasExactSynonym", + "val" : "predominantly white regional part of diencephalon", + "xrefs" : [ "BIRNLEX:1678" ] }, { - "val" : "MA:0000015" + "pred" : "hasExactSynonym", + "val" : "white matter of diencephalon", + "xrefs" : [ "FMA:83931" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:1678" }, { - "val" : "SCTID:71616004" + "val" : "FMA:83931" }, { - "val" : "TAO:0005145" + "val" : "TAO:0000338" }, { - "val" : "VHOG:0001245" + "val" : "ZFA:0000338" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0023148" }, { - "val" : "XAO:0000172" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004022", + "lbl" : "germinal neuroepithelium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.", + "xrefs" : [ "MP:0004261", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "germinal neuroepithelial layer", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "ZFA:0005145" + "pred" : "hasExactSynonym", + "val" : "germinal neuroepithelium", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { - "val" : "galen:Muscle" + "pred" : "hasExactSynonym", + "val" : "original neural tube", + "xrefs" : [ "NCBIBook:NBK10047" ] } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -21493,874 +24659,834 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001711", - "lbl" : "eyelid", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004060", + "lbl" : "neural tube ventricular layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.", + "xrefs" : [ "MP:0009689", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blepharon" + "pred" : "hasBroadSynonym", + "val" : "ependymal layer", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { "pred" : "hasExactSynonym", - "val" : "eye lid" + "val" : "neural tube ependymal layer", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { "pred" : "hasExactSynonym", - "val" : "palpebra" + "val" : "neural tube ventricular germinal zone", + "xrefs" : [ "NCBIBook:NBK10047" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "blephara" + "pred" : "hasExactSynonym", + "val" : "neural tube ventricular zone", + "xrefs" : [ "MP:0009689" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "palpebrae" + "pred" : "hasNarrowSynonym", + "val" : "neural tube ependymal zone", + "xrefs" : [ "MP:0009689" ] } ], "xrefs" : [ { - "val" : "BTO:0002241" - }, { - "val" : "EHDAA2:0000487" - }, { - "val" : "EHDAA:9037" - }, { - "val" : "EMAPA:17829" - }, { - "val" : "EV:0100338" - }, { - "val" : "FMA:54437" - }, { - "val" : "GAID:72" - }, { - "val" : "MA:0000268" - }, { - "val" : "MESH:D005143" - }, { - "val" : "NCIT:C12713" - }, { - "val" : "SCTID:265782007" + "val" : "EMAPA:17152" }, { - "val" : "UMLS:C0015426" + "val" : "EMAPA:35362" }, { - "val" : "VHOG:0000016" + "val" : "EMAPA_RETIRED:16783" }, { - "val" : "Wikipedia:Eyelid" + "val" : "MA:0003193" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001766", - "lbl" : "anterior chamber of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004061", + "lbl" : "neural tube mantle layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens.", - "xrefs" : [ "MESH:A09.371.060.067", "MP:0005205" ] + "val" : "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.", + "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "anterior chamber", - "xrefs" : [ "HP:0000593", "MP:0010709" ] + "val" : "neural tube intermediate zone", + "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] }, { - "pred" : "hasExactSynonym", - "val" : "anterior chamber of eye" + "pred" : "hasRelatedSynonym", + "val" : "future brain marginal layer", + "xrefs" : [ "EMAPA:35360" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:17148" }, { - "pred" : "hasExactSynonym", - "val" : "camera anterior" + "val" : "EMAPA:35360" }, { + "val" : "neuronames:1367" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004062", + "lbl" : "neural tube marginal layer", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.", + "xrefs" : [ "MP:0009691", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "eye anterior chamber" - }, { - "pred" : "hasRelatedSynonym", - "val" : "camera anterior bulbi", - "xrefs" : [ "BTO:0002084" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "camera anterior bulbi oculi", - "xrefs" : [ "Wikipedia:Anterior_chamber_of_eyeball" ] + "val" : "neural tube marginal zone", + "xrefs" : [ "MP:0009691" ] }, { "pred" : "hasRelatedSynonym", - "val" : "camera oculi anterior", - "xrefs" : [ "BTO:0002084" ] + "val" : "brain marginal zone" } ], "xrefs" : [ { - "val" : "BTO:0002084" - }, { - "val" : "EHDAA2:0000129" - }, { - "val" : "EHDAA:9033" - }, { - "val" : "EMAPA:18231" - }, { - "val" : "FMA:58078" - }, { - "val" : "GAID:889" - }, { - "val" : "MA:0000262" - }, { - "val" : "MESH:D000867" - }, { - "val" : "NCIT:C12667" - }, { - "val" : "SCTID:181160009" - }, { - "val" : "UMLS:C0003151" - }, { - "val" : "VHOG:0001431" + "val" : "EMAPA:17151" }, { - "val" : "Wikipedia:Anterior_chamber_of_eyeball" + "val" : "neuronames:1368" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - 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"val" : "tunica vasculosa of eyeball", - "xrefs" : [ "FMA:58103" ] + "val" : "content of orbital part of eye", + "xrefs" : [ "FMA:260119" ] }, { "pred" : "hasExactSynonym", - "val" : "uvea", - "xrefs" : [ "FMA:58103" ] + "val" : "eye region", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "uveal tract", - "xrefs" : [ "FMA:58103" ] + "val" : "orbital part of face", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "pars iridica retinae", - "xrefs" : [ "Wikipedia:Uvea" ] + "val" : "ocular and peri-ocular region" }, { "pred" : "hasRelatedSynonym", - "val" : "tunica vasculatis oculi", - "xrefs" : [ "Wikipedia:Uvea" ] + "val" : "ocular region" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "tunica vasculosa bulbi", - "xrefs" : [ "Wikipedia:Uvea" ] + "val" : "orbital content", + "xrefs" : [ "FMA:260119" ] }, { "pred" : "hasRelatedSynonym", - 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Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].", + "xrefs" : [ "GO:0003404", "Wikipedia:Optic_vesicles" ] + }, + "comments" : [ "Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 \"Developmental Biology\"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "endothelium anterius corneae", - "xrefs" : [ "BTO:0000287" ] + "val" : "evagination" }, { "pred" : "hasRelatedSynonym", - "val" : "endothelium camerae anterioris bulbi", - "xrefs" : [ "BTO:0000287" ] + "val" : "eye vesicle", + "xrefs" : [ "XAO:0000228" ] }, { "pred" : "hasRelatedSynonym", - "val" : "endothelium corneale", - "xrefs" : [ "BTO:0000287" ] + "val" : "ocular vesicle", + "xrefs" : [ "VHOG:0000165" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "epithelium posterius corneae", - "xrefs" : [ "BTO:0000287" ] + "val" : "optic vesicles", + "xrefs" : [ "ZFA:0000050" ] } ], "xrefs" : [ { - "val" : "BTO:0000287" - }, { - "val" : "CALOHA:TS-0173" - }, { - "val" : "EFO:0001917" - }, { - "val" : "EHDAA2:0000319" + "val" : "AAO:0011039" }, { - "val" : "EMAPA:17162" + "val" : "EHDAA2:0001320" }, { - "val" : "FMA:58263" + "val" : "EMAPA:16540" }, { - "val" : "GAID:895" + "val" : "FMA:293357" }, { - "val" : "MA:0001243" + "val" : "NCIT:C34236" }, { - "val" : "MESH:D019573" + "val" : "SCTID:362864008" }, { - "val" : "NCIT:C12928" + "val" : "TAO:0000050" }, { - "val" : "SCTID:368825001" + "val" : "UMLS:C0231106" }, { - "val" : "TAO:0002187" + "val" : "VHOG:0000165" }, { - "val" : "UMLS:C0459875" + "val" : "Wikipedia:Optic_vesicles" }, { - "val" : "Wikipedia:Corneal_epithelium" + "val" : "XAO:0000228" }, { - "val" : "ZFA:0001683" + "val" : "ZFA:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" + "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001773", - "lbl" : "sclera", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", + "lbl" : "cardiogenic plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].", - "xrefs" : [ "Wikipedia:Sclera", "ZFIN:ZDB-PUB-050701-15" ] + "val" : "The first recognizable structure derived from the heart field.", + "xrefs" : [ "GO:0003142" ] }, - "comments" : [ "Disease notes: implicated in rheumatoid arthritis." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "scleral capsule" - } ], - "xrefs" : [ { - "val" : "AAO:0010354" - }, { - "val" : "BTO:0001606" - }, { - "val" : "EMAPA:19027" - }, { - "val" : "EV:0100342" - }, { - "val" : "FMA:58269" - }, { - "val" : "GAID:911" - }, { - "val" : "MA:0000280" - }, { - "val" : "MESH:D012590" - }, { - "val" : "NCIT:C12784" - }, { - "val" : "SCTID:181163006" + "pred" : "hasExactSynonym", + "val" : "myocardial plate", + "xrefs" : [ "EHDAA2:0000215" ] }, { - "val" : "UMLS:C0036410" + "pred" : "hasRelatedSynonym", + "val" : "cardiac crescent", + "xrefs" : [ "EMAPA:16106" ] }, { - "val" : "VHOG:0001274" + "pred" : "hasRelatedSynonym", + "val" : "cardiogenic crescent", + "xrefs" : [ "GO:0003142" ] }, { - "val" : "Wikipedia:Sclera" + "pred" : "hasRelatedSynonym", + "val" : "heart rudiment" + } ], + "xrefs" : [ { + "val" : "EHDAA2:0000215" }, { - "val" : "XAO:0000183" + "val" : "EMAPA:16106" }, { - "val" : "ZFA:0005563" + "val" : "VHOG:0000975" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. 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Along with the ciliary body and iris, the choroid forms the uveal tract[WP].", - "xrefs" : [ "Wikipedia:Choroid" ] + "val" : "An epithelial tube that will give rise to the mature heart.", + "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "choroid", - "xrefs" : [ "MA:0000263" ] - }, { - "pred" : "hasExactSynonym", - "val" : "choroid coat", - "xrefs" : [ "Wikipedia:Choroid" ] - }, { - "pred" : "hasExactSynonym", - "val" : "choroidea", - "xrefs" : [ "Wikipedia:Choroid" ] + "val" : "embryonic heart tube", + "xrefs" : [ "GO:0003143" ] }, { "pred" : "hasExactSynonym", - "val" : "eye choroid", - "xrefs" : [ "VHOG:0001568" ] + "val" : "endocardial heart tube", + "xrefs" : [ "MP:0012700" ] }, { "pred" : "hasExactSynonym", - "val" : "posterior uvea", - "xrefs" : [ "Wikipedia:Uvea#Regions" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "chorioid", - "xrefs" : [ "BTO:0001829" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "choroidea", - "xrefs" : [ "Wikipedia:Choroid" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "optic choroid", - "xrefs" : [ "ZFA:0005229" ] + "val" : "endocardial tube", + "xrefs" : [ "XAO:0000337" ] } ], "xrefs" : [ { - "val" : "BTO:0001829" - }, { - "val" : "CALOHA:TS-2054" - }, { - "val" : "EMAPA:19077" - }, { - "val" : "EV:0100347" - }, { - "val" : "FMA:58298" + "val" : "AAO:0010411" }, { - "val" : "GAID:913" + "val" : "EFO:0003526" }, { - "val" : "MA:0000263" + "val" : "EMAPA:32685" }, { - "val" : "MESH:D002829" + "val" : "NCIT:C34161" }, { - "val" : "NCIT:C12344" + "val" : "TAO:0000360" }, { - "val" : "SCTID:181172003" + "val" : "XAO:0000337" }, { - "val" : "TAO:0005229" + "val" : "ZFA:0000360" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "lbl" : "cardiac chamber", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", + "xrefs" : [ "GO:0003205" ] + }, + "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "chamber of heart" }, { - "val" : "UMLS:C0008520" + "pred" : "hasExactSynonym", + "val" : "heart chamber" + } ], + "xrefs" : [ { + "val" : "FMA:7095" }, { - "val" : "VHOG:0001568" + "val" : "SCTID:276456008" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004277", + "lbl" : "eye muscle", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A muscle that is part of the eye region.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "AAO:0000156" }, { - "val" : "Wikipedia:Choroid" + "val" : "EMAPA:35335" }, { - "val" : "ZFA:0005229" + "val" : "MA:0000271" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. 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The heart rudiment is the first structure of the heart tube.", + "xrefs" : [ "GO:0003313" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "ciliary body epithelium", - "xrefs" : [ "FMA:58464" ] - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of ciliary body", - "xrefs" : [ "FMA:58464" ] + "val" : "heart cone", + "xrefs" : [ "GO:0003313" ] }, { "pred" : "hasExactSynonym", - "val" : "ocular ciliary epithelium" + "val" : "rudimentary heart", + "xrefs" : [ "ZFA:0000115" ] } ], "xrefs" : [ { - "val" : "BTO:0001770" - }, { - "val" : "CALOHA:TS-0695" - }, { - "val" : "EMAPA:35239" - }, { - "val" : "FMA:58464" - }, { - "val" : "MA:0001238" + "val" : "TAO:0000115" }, { - "val" : "NCIT:C32314" + "val" : "ZFA:0000115" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004348", + "lbl" : "optic eminence", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The embryonic structure that gives rise to the corneal ectoderm.", + "xrefs" : [ "MP:0006305" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "EHDAA:938" }, { - "val" : "SCTID:280870004" + "val" : "EMAPA:16322" }, { - "val" : "UMLS:C0459736" + "val" : "RETIRED_EHDAA2:0001308" }, { - "val" : "Wikipedia:Ciliary_body#Ciliary_epithelium" + "val" : "VHOG:0001296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001781", - "lbl" : "layer of retina", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004367", + "lbl" : "Descemet's membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the layers that make up the retina[MP].", - "xrefs" : [ "MP:0003727" ] + "val" : "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].", + "xrefs" : [ "MP:0004285", "https://github.com/obophenotype/uberon/issues/15" ] }, + "comments" : [ "The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)" ], "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "retina layer" + "val" : "Descemet membrane" }, { "pred" : "hasExactSynonym", - "val" : "retina neuronal layer", - "xrefs" : [ "MP:0006069" ] + "val" : "Descemet's posterior elastic lamina", + "xrefs" : [ "FMA:58309" ] }, { "pred" : "hasExactSynonym", - "val" : "retinal layer" + "val" : "lamina limitans posterior", + "xrefs" : [ "FMA:58309" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "retinal neuronal layer", - "xrefs" : [ "MP:0006069" ] + "val" : "lamina limitans posterior corneae", + "xrefs" : [ "FMA:58309", "FMA:TA" ] + }, { + "pred" : "hasExactSynonym", + "val" : "posterior limiting lamina", + "xrefs" : [ "MA:0001246" ] + }, { + "pred" : "hasExactSynonym", + "val" : "posterior limiting lamina of cornea", + "xrefs" : [ "FMA:58309" ] + }, { + "pred" : "hasExactSynonym", + "val" : "posterior limiting membrane", + "xrefs" : [ "ZFA:0001686" ] } ], "xrefs" : [ { - 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Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001795", - "lbl" : "inner plexiform layer of retina", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", + "lbl" : "muscle structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia).", - "xrefs" : [ "NLX:20558" ] + "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", + "xrefs" : [ "GO:0061061" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "retina inner plexiform layer" - }, { - "pred" : "hasExactSynonym", - "val" : "retinal inner plexiform layer" - }, { - "pred" : "hasExactSynonym", - "val" : "stratum plexiforme internum", - "xrefs" : [ "FMA:58704" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasNarrowSynonym", - "val" : "IPL" - }, { - "pred" : "hasRelatedSynonym", - "val" : "inner plexiform layer", - "xrefs" : [ "BTO:0003175" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "internal plexiform layer of retina", - "xrefs" : [ "NLXANAT:1005032" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "retina, inner plexiform layer", - "xrefs" : [ "BAMS:Ripl" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "retinal internal plexiform layer", - "xrefs" : [ "NLXANAT:1005032" ] + "val" : "musculus", + "xrefs" : [ "FMA:30316" ] }, { "pred" : "hasRelatedSynonym", - "val" : "stratum plexifome internum", - "xrefs" : [ "BTO:0003175" ] + "val" : "muscle" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "stratum plexiforme internum retinae", - "xrefs" : [ "Wikipedia:Inner_plexiform_layer" ] + "val" : "muscle element" } ], "xrefs" : [ { - "val" : "BAMS:Ripl" - }, { - "val" : "BTO:0003175" - }, { - "val" : "EMAPA:35741" - }, { - "val" : "FMA:58704" - }, { - "val" : "MA:0001312" - }, { - "val" : "NCIT:C32809" - }, { - "val" : "NLX:20558" - }, { - "val" : "NLXANAT:1005032" - }, { - "val" : "SCTID:280682006" - }, { - "val" : "TAO:0001329" - }, { - "val" : "UMLS:C0229221" - }, { - "val" : "VHOG:0001168" - }, { - "val" : "Wikipedia:Inner_plexiform_layer" - }, { - "val" : "XAO:0003225" - }, { - "val" : "ZFA:0001329" + "val" : "FMA:30316" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001796", - "lbl" : "aqueous humor of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", + "lbl" : "epithelial fold", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A thick watery refractive medium that fills the space between the lens and the cornea[WP].", - "xrefs" : [ "Wikipedia:Aqueous_humor" ] + "val" : "An epithelial sheet bent on a linear axis.", + "xrefs" : [ "GO:0060571" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005162", + "lbl" : "multi cell part structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.", + "xrefs" : [ "CARO:0001000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "aqueous humor" + "val" : "multi-cell-component structure", + "xrefs" : [ "CARO:0001000" ] }, { "pred" : "hasExactSynonym", - "val" : "aqueous humour", - "xrefs" : [ "EHDAA2:0000139" ] + "val" : "multi-cell-part structure", + "xrefs" : [ "CARO:0001000" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "humor aquosus", - "xrefs" : [ "FMA:58819", "FMA:TA" ] + "pred" : "hasRelatedSynonym", + "val" : "cell part cluster", + "xrefs" : [ "FMA:83115" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0000139" - }, { - "val" : "EHDAA:10196" - }, { - "val" : "EMAPA:18232" - }, { - "val" : "ENVO:02000024" - }, { - "val" : "FMA:58819" - }, { - "val" : "GAID:890" - }, { - "val" : "MA:0001236" - }, { - "val" : "MESH:D001082" - }, { - "val" : "NCIT:C13190" - }, { - "val" : "SCTID:280587006" - }, { - "val" : "UMLS:C0003662" + "val" : "AAO:0011000" }, { - "val" : "VHOG:0000548" + "val" : "CARO:0001000" }, { - "val" : "Wikipedia:Aqueous_humor" + "val" : "FBbt:00007060" }, { - "val" : "ZFA:0005564" + "val" : "FMA:83115" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001797", - "lbl" : "vitreous humor", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005174", + "lbl" : "dorsal region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina.", - "xrefs" : [ "MP:0002699" ] + "val" : "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "portion of vitreous humor", - "xrefs" : [ "FMA:67388" ] - }, { - "pred" : "hasExactSynonym", - "val" : "humor vitreous" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "humor vitreus", - "xrefs" : [ "FMA:58822", "FMA:TA" ] - }, { "pred" : "hasExactSynonym", - "val" : "vitreous", - "xrefs" : [ "ZFA:0005561" ] + "val" : "back organ", + "xrefs" : [ "MA:0001901" ] }, { "pred" : "hasExactSynonym", - "val" : "whole portion of vitreous humor", - "xrefs" : [ "FMA:58822" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "humoral fluid", - "xrefs" : [ "BTO:0001451" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular fluid", - "xrefs" : [ "BTO:0001451" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "vitreous fluid", - "xrefs" : [ "BTO:0001451" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "vitreous humour" + "val" : "dorsal region organ" } ], "xrefs" : [ { - "val" : "BTO:0001451" - }, { - "val" : "CALOHA:TS-0308" - }, { - "val" : "EMAPA:17837" - }, { - "val" : "ENVO:02000032" - }, { - "val" : "EV:0100344" - }, { - "val" : "FMA:58822" - }, { - "val" : "MA:0001286" - }, { - "val" : "NCIT:C13323" - }, { - "val" : "UMLS:C0229096" - }, { - "val" : "VHOG:0000795" - }, { - "val" : "Wikipedia:Vitreous_humour" + "val" : "EMAPA:37274" }, { - "val" : "ZFA:0005561" + "val" : "MA:0001901" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001798", - "lbl" : "vitreous body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", + "lbl" : "trunk region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified].", - "xrefs" : [ "MP:0002699" ] + "val" : "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "trunk organ", + "xrefs" : [ "MA:0000516" ] + } ], "xrefs" : [ { - "val" : "CALOHA:TS-0308" - }, { - "val" : "FMA:58827" - }, { - "val" : "GAID:919" - }, { - "val" : "MA:0002462" - }, { - "val" : "MESH:D014822" - }, { - "val" : "NCIT:C33884" - }, { - "val" : "SCTID:181170006" + "val" : "EMAPA:37270" }, { - "val" : "UMLS:C0042905" + "val" : "MA:0000516" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001799", - "lbl" : "vitreous chamber of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005178", + "lbl" : "thoracic cavity element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified].", - "xrefs" : [ "BTO:0002087" ] + "val" : "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "camera postrema", - "xrefs" : [ "FMA:58848" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "camera postrema bulbi oculi", - "xrefs" : [ "FMA:58848", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "camera vitrea", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "camera vitrea bulbi", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "postremal chamber", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "postremal chamber of eyeball", - "xrefs" : [ "FMA:58848" ] - }, { - "pred" : "hasExactSynonym", - "val" : "vitreous chamber", - "xrefs" : [ "FMA:58848" ] + "val" : "thoracic cavity organ", + "xrefs" : [ "MA:0000557" ] } ], "xrefs" : [ { - "val" : "BTO:0002087" - }, { - "val" : "EMAPA:37805" - }, { - "val" : "FMA:58848" - }, { - "val" : "MA:0002461" - }, { - "val" : "NCIT:C33885" - }, { - "val" : "UMLS:C0229095" + "val" : "EMAPA:37273" }, { - "val" : "Wikipedia:Vitreous_chamber" + "val" : "MA:0000557" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -23352,273 +26308,152 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "lbl" : "anterior segment of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", + "lbl" : "thoracic segment organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive).", - "xrefs" : [ "ISBN:0-683-40008-8", "MESH:A09.371.060", "MP:0005193" ] + "val" : "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "anterior eye segment" - }, { - "pred" : "hasExactSynonym", - "val" : "anterior segment eye", - "xrefs" : [ "ZFA:0005566" ] - }, { - "pred" : "hasExactSynonym", - "val" : "anterior segment of eye" - }, { - "pred" : "hasExactSynonym", - "val" : "anterior segment of the eye" - }, { - "pred" : "hasExactSynonym", - "val" : "eye anterior segment" - }, { - "pred" : "hasExactSynonym", - "val" : "segmentum anterius (bulbus oculi)" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "segmentum anterius bulbi oculi", - "xrefs" : [ "Wikipedia:Anterior_segment_of_eyeball" ] + "val" : "upper body organ", + "xrefs" : [ "MA:0000563" ] } ], - "xrefs" : [ { - "val" : "EMAPA:36594" - }, { - "val" : "FMA:58865" - }, { - "val" : "MA:0002484" - }, { - "val" : "MESH:D000869" - }, { - "val" : "NCIT:C12668" - }, { - "val" : "SCTID:280658001" - }, { - "val" : "UMLS:C0003153" - }, { - "val" : "Wikipedia:Anterior_segment_of_eyeball" + "xrefs" : [ { + "val" : "EMAPA:37271" }, { - "val" : "ZFA:0005566" + "val" : "MA:0000563" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001802", - "lbl" : "posterior segment of eyeball", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005253", + "lbl" : "head mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive).", - "xrefs" : [ "ISBN:0-683-40008-8", "MP:0005195" ] + "val" : "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.", + "xrefs" : [ "ISBN:0683400088", "MP:0011260" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "eye posterior segment" - }, { - "pred" : "hasExactSynonym", - "val" : "posterior eye segment" - }, { - "pred" : "hasExactSynonym", - "val" : "posterior segment eye", - "xrefs" : [ "ZFA:0005567" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior segment of eye" - }, { - "pred" : "hasExactSynonym", - "val" : "posterior segment of the eye" + "val" : "cephalic mesenchyme", + "xrefs" : [ "MP:0011260" ] }, { - "pred" : "hasExactSynonym", - "val" : "segmentum posterius (bulbus oculi)" + "pred" : "hasRelatedSynonym", + "val" : "cranial mesenchyme", + "xrefs" : [ "MGI:anna" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "pred" : "hasRelatedSynonym", - 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Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA].", + "xrefs" : [ "FMA:9689", "https://github.com/obophenotype/uberon/issues/86" ] + }, + "comments" : [ "See notes for serous membrane" ], + "xrefs" : [ { + "val" : "FMA:9689" }, { - "val" : "MESH:D008526" + "val" : "SCTID:362890006" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005908", + "lbl" : "conjunctival sac", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A serous sac which is the aggregate of the conjunctiva plus the conjunctival space.", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/Serous-Membranes-Design-Pattern" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "conjunctiva serous sac" }, { - "val" : "MIAA:0000111" + "pred" : "hasNarrowSynonym", + "val" : "subbrillar sac", + "xrefs" : [ "NCBITaxon:8570" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:18233" }, { - "val" : "NCIT:C12442" + "val" : "FMA:20291" }, { - "val" : "SCTID:279104005" + "val" : "SCTID:362531001" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005944", + "lbl" : "axial skeleton plus cranial skeleton", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].", + "xrefs" : [ "FMA:71221", "VSAO:0000056", "Wikipedia:Axial_skeleton", "https://github.com/obophenotype/uberon/issues/44", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "skeleton axiale", + "xrefs" : [ "Wikipedia:Axial_skeleton" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000963" }, { - "val" : "TAO:0000545" + "val" : "EMAPA:17214" }, { - "val" : "UMLS:C0025148" + "val" : "MA:0000308" }, { - "val" : "UMLS:C1269575" + "val" : "NCIT:C32172" }, { - "val" : "VHOG:0000181" + "val" : "SCTID:361725000" }, { - "val" : "Wikipedia:Bone_marrow_of_ovary_oblongata" + "val" : "UMLS:C0222645" }, { - "val" : "XAO:0003100" + "val" : "VSAO:0000056" }, { - "val" : "ZFA:0000545" + "val" : "Wikipedia:Axial_skeleton" }, { - "val" : "neuronames:698" + "val" : "XAO:0004011" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -23946,712 +27020,640 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001908", - "lbl" : "optic tract", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006134", + "lbl" : "nerve fiber", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. 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A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system.", + "xrefs" : [ "Wikipedia:Nervous_system_fiber" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "optic lemniscus" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "optic tracts", - "xrefs" : [ "ZFA:0000252" ] + "val" : "nerve fibre", + "xrefs" : [ "FMA:5914" ] }, { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tractus optici", - "xrefs" : [ "NeuroNames:460" ] + "pred" : "hasExactSynonym", + "val" : "neurofibra", + "xrefs" : [ "FMA:5914", "FMA:TA" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "neurofibrum", + "xrefs" : [ "FMA:5914" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "tractus opticus", - "xrefs" : [ "Wikipedia:Optic_tract" ] + "val" : "nerve fibers", + "xrefs" : [ "BAMS:nfi" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "visual pathway", - "xrefs" : [ "GAID:735" ] + "val" : "neurofibra", + "xrefs" : [ "Wikipedia:Nerve_fiber" ] } ], "xrefs" : [ { - "val" : "BAMS:opt" + "val" : "BAMS:nfi" }, { - "val" : "BIRNLEX:1684" + "val" : "FMA:5914" }, { - "val" : "BM:Tel-OT" + "val" : "MESH:D009412" }, { - "val" : "DHBA:10589" + "val" : "SCTID:88545005" }, { - "val" : "DMBA:17785" + "val" : "Wikipedia:Nervous_system_fiber" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "EMAPA:35617" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006135", + "lbl" : "myelinated nerve fiber", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH).", + "xrefs" : [ "ncithesaurus:Myelinated_Nerve_Fiber" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "FMA:5915" }, { - "val" : "FMA:62046" + "val" : "GAID:745" }, { - "val" : "GAID:735" + "val" : "MESH:D009413" }, { - "val" : "HBA:9309" + "val" : "NCIT:C12627" }, { - "val" : "MA:0001099" + "val" : "SCTID:362296008" }, { - "val" : "MBA:125" + "val" : "UMLS:C0027750" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adding link to UBERON:0002316 ! white matter of neuraxis" }, { - "val" : "MESH:D014795" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117569" }, { - "val" : "NCIT:C33218" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" }, { - "val" : "SCTID:280952003" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" }, { - "val" : "TAO:0000252" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006222", + "lbl" : "future diencephalon", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The foremost region of the future forebrain that develops into the diencephalon.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Diencephalon" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "presumptive diencephalon", + "xrefs" : [ "TAO:0000574" ] + } ], + "xrefs" : [ { + "val" : "EFO:0003442" }, { - "val" : "UMLS:C0152405" + "val" : "EHDAA2:0000600" }, { - "val" : "VHOG:0001164" + "val" : "EHDAA:844" }, { - "val" : "Wikipedia:Optic_tract" + "val" : "EMAPA:16514" }, { - "val" : "XAO:0004101" + "val" : "RETIRED_EHDAA2:0000386" }, { - "val" : "ZFA:0000252" + "val" : "TAO:0000574" }, { - "val" : "neuronames:460" + "val" : "ZFA:0000574" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001943", - "lbl" : "midbrain tegmentum", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006238", + "lbl" : "future brain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].", - "xrefs" : [ "FMA:FMA", "ISBN:0471888893", "Wikipedia:Midbrain_tegmentum" ] + "val" : "The embryonic precursor of the brain.", + "xrefs" : [ "NLX:94995" ] }, - "comments" : [ "'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasBroadSynonym", - "val" : "MTg", - "xrefs" : [ "BIRNLEX:1200", "NIFSTD:NeuroNames_abbrevSource" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "tegmentum", - "xrefs" : [ "ISBN:0471888893" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "tegmentum mesencephali", - "xrefs" : [ "Wikipedia:Midbrain_tegmentum" ] + "val" : "brain rudiment", + "xrefs" : [ "TAO:0000146" ] }, { "pred" : "hasExactSynonym", - "val" : "tegmentum of midbrain" + "val" : "presumptive brain", + "xrefs" : [ "ZFA:0000146" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "mesencephalic tegmentum", - "xrefs" : [ "VHOG:0001367" ] + "pred" : "hasNarrowSynonym", + "val" : "encephalon", + "xrefs" : [ "NLX:94995" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "tegmentum mesencephalicum", - "xrefs" : [ "NeuroNames:491" ] + "val" : "embryonic brain", + "xrefs" : [ "BTO:0004726" ] } ], "xrefs" : [ { - "val" : "BAMS:MTg" - }, { - "val" : "BIRNLEX:1200" - }, { - "val" : "BTO:0003388" - }, { - "val" : "DHBA:12195" - }, { - "val" : "EFO:0000921" - }, { - "val" : "EHDAA2:0004475" - }, { - "val" : "EMAPA:18215" - }, { - "val" : "FMA:62393" - }, { - "val" : "HBA:9002" - }, { - "val" : "MA:0000212" + "val" : "BAMS:Enc" }, { - "val" : "MAT:0000452" + "val" : "BTO:0004726" }, { - "val" : "SCTID:362392007" + "val" : "EFO:0003431" }, { - "val" : "TAO:0000160" + "val" : "EHDAA:300" }, { - "val" : "UMLS:C0039441" + "val" : "EHDAA:830" }, { - "val" : "VHOG:0001367" + "val" : "EMAPA:16089" }, { - "val" : "Wikipedia:Midbrain_tegmentum" + "val" : "FMA:312967" }, { - "val" : "XAO:0004271" + "val" : "RETIRED_EHDAA2:0000591" }, { - "val" : "ZFA:0000160" + "val" : "TAO:0000146" }, { - "val" : "neuronames:491" + "val" : "ZFA:0000146" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "lbl" : "blood plasma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006240", + "lbl" : "future forebrain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The liquid component of blood, in which erythrocytes are suspended.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A presumptive structure that has the potential to develop into a forebrain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "plasma", - "xrefs" : [ "MA:0002501" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "portion of plasma", - "xrefs" : [ "FMA:62970" ] + "pred" : "hasExactSynonym", + "val" : "future prosencephalon" }, { "pred" : "hasExactSynonym", - "val" : "blood plasm" + "val" : "presumptive forebrain", + "xrefs" : [ "ZFA:0000062" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of blood plasma" + "val" : "presumptive prosencephalon", + "xrefs" : [ "TAO:0000062" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "prosencephalon", + "xrefs" : [ "EHDAA2:0000661" ] } ], "xrefs" : [ { - "val" : "BTO:0000131" - }, { - "val" : "CALOHA:TS-0800" - }, { - "val" : "EFO:0001905" - }, { - "val" : "EMAPA:35690" - }, { - "val" : "FMA:62970" - }, { - "val" : "GAID:1178" + "val" : "BAMS:Pros" }, { - "val" : "MA:0002501" + "val" : "EFO:0003423" }, { - "val" : "MAT:0000052" + "val" : "EHDAA2:0000661" }, { - "val" : "MESH:D010949" + "val" : "EHDAA:2643" }, { - "val" : "MIAA:0000052" + "val" : "EMAPA:16640" }, { - "val" : "NCIT:C13356" + "val" : "TAO:0000062" }, { - "val" : "UMLS:C0032105" + "val" : "Wikipedia:Prosencephalon" }, { - "val" : "Wikipedia:Blood_plasma" + "val" : "ZFA:0000062" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "lbl" : "blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006241", + "lbl" : "future spinal cord", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A vessel through which blood circulates in the body.", - "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "vascular element", - "xrefs" : [ "EMAPA:35993" ] + "pred" : "hasExactSynonym", + "val" : "presumptive spinal cord", + "xrefs" : [ "ZFA:0000417" ] }, { "pred" : "hasExactSynonym", - "val" : "region of vascular tree organ", - "xrefs" : [ "FMA:50722" ] + "val" : "presumptive spinal cord neural keel", + "xrefs" : [ "TAO:0000417" ] }, { "pred" : "hasExactSynonym", - "val" : "vascular tree organ region", - "xrefs" : [ "FMA:50722" ] + "val" : "presumptive spinal cord neural plate", + "xrefs" : [ "TAO:0000417" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "vas sanguineum", - "xrefs" : [ "Wikipedia:Blood_vessel" ] + "pred" : "hasExactSynonym", + "val" : "presumptive spinal cord neural rod", + "xrefs" : [ "TAO:0000417" ] } ], "xrefs" : [ { - "val" : "AAO:0011004" - }, { - "val" : "AEO:0000207" - }, { - "val" : "BTO:0001102" - }, { - "val" : "CALOHA:TS-0080" - }, { - "val" : "EFO:0000817" + "val" : "EFO:0003438" }, { - "val" : "EHDAA2:0003252" + "val" : "EHDAA2:0000674" }, { - "val" : "EHDAA:240" + "val" : "EHDAA:898" }, { - "val" : "EMAPA:32743" + "val" : "EMAPA:16092" }, { - "val" : "EMAPA:35993" + "val" : "EMAPA:16755" }, { - "val" : "FMA:50722" + "val" : "TAO:0000417" }, { - "val" : "FMA:63183" + "val" : "ZFA:0000417" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", + "lbl" : "notochordal plate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", + "xrefs" : [ "VHOG:0001212" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], + "xrefs" : [ { + "val" : "EHDAA2:0001278" }, { - "val" : "GAID:169" + "val" : "EHDAA:264" }, { - "val" : "MA:0000060" + "val" : "EMAPA:16101" }, { - "val" : "MAT:0000393" + "val" : "NCIT:C34231" }, { - "val" : "MESH:D001808" + "val" : "UMLS:C1518429" }, { - "val" : "NCIT:C12679" + "val" : "VHOG:0001212" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ordering; awaiting confirmation from JB" }, { - "val" : "NLXANAT:090901" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", + "lbl" : "notochordal process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", + "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] + }, + "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "chordamesoderm" }, { - "val" : "SCTID:361097006" + "pred" : "hasRelatedSynonym", + "val" : "presumptive notochord" + } ], + "xrefs" : [ { + "val" : "EHDAA2:0001279" }, { - "val" : "TAO:0002137" + "val" : "EHDAA:224" }, { - "val" : "UMLS:C0005847" + "val" : "EMAPA:16102" }, { - "val" : "VHOG:0001250" + "val" : "FMA:293135" }, { - "val" : "Wikipedia:Blood_vessel" + "val" : "NCIT:C34232" }, { - "val" : "XAO:0001011" + "val" : "UMLS:C1518430" }, { - "val" : "ZFA:0005314" + "val" : "VHOG:0001213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001985", - "lbl" : "corneal endothelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006311", + "lbl" : "chamber of eyeball", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].", - "xrefs" : [ "Wikipedia:Corneal_endothelium" ] + "val" : "A segment of the eyeball that is filled with refractive media.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "cornea endothelium", - "xrefs" : [ "OBOL:automatic" ] + "val" : "eye chamber", + "xrefs" : [ "MA:0002459" ] }, { "pred" : "hasExactSynonym", - "val" : "endothelium of cornea", - "xrefs" : [ "OBOL:automatic" ] + "val" : "eyeball chamber", + "xrefs" : [ "FMA:58071" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "epithelium posterius corneae", - "xrefs" : [ "Wikipedia:Corneal_endothelium" ] + "val" : "chamber of eye", + "xrefs" : [ "BTO:0002085" ] } ], "xrefs" : [ { - "val" : "CALOHA:TS-0172" - }, { - "val" : "EMAPA:35935" - }, { - "val" : "FMA:63882" - }, { - "val" : "GAID:891" - }, { - "val" : "MA:0001242" - }, { - "val" : "MESH:D004728" + "val" : "BTO:0002085" }, { - "val" : "NCIT:C12707" + "val" : "EMAPA:37529" }, { - "val" : "SCTID:368827009" + "val" : "FMA:58071" }, { - "val" : "TAO:0002186" + "val" : "MA:0002459" }, { - "val" : "UMLS:C0014259" + "val" : "NCIT:C32301" }, { - "val" : "Wikipedia:Corneal_endothelium" + "val" : "SCTID:280540004" }, { - "val" : "ZFA:0001687" + "val" : "UMLS:C0459556" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "lbl" : "endothelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006312", + "lbl" : "ocular refractive media", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA].", - "xrefs" : [ "FMA:63916", "MESH:A10.272.491", "https://github.com/obophenotype/uberon/issues/225" ] + "val" : "Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "xrefs" : [ { - "val" : "BTO:0000393" - }, { - "val" : "CALOHA:TS-0278" - }, { - "val" : "EFO:0002548" - }, { - "val" : "FMA:63916" - }, { - "val" : "GAID:520" - }, { - "val" : "MESH:D004727" - }, { - "val" : "NCIT:C12481" - }, { - "val" : "SCTID:27168002" - }, { - "val" : "UMLS:C0014257" - }, { - "val" : "galen:Endothelium" + "val" : "MA:0001911" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002020", - "lbl" : "gray matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006314", + "lbl" : "bodily fluid", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.", - "xrefs" : [ "Wikipedia:Gray_matter", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", + "xrefs" : [ "MESH:A12.207", "Wikipedia:Body_fluid" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gray matter" + "pred" : "hasBroadSynonym", + "val" : "fluid" }, { "pred" : "hasExactSynonym", - "val" : "gray matter of neuraxis", - "xrefs" : [ "FMA:67242" ] + "val" : "body fluid", + "xrefs" : [ "GAID:266" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:20" }, { - "pred" : "hasExactSynonym", - "val" : "grey matter" + "val" : "EMAPA:37441" }, { - 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Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracolumbar region" - }, { - "pred" : "hasExactSynonym", - "val" : "torso" - }, { - "pred" : "hasExactSynonym", - "val" : "trunk region", - "xrefs" : [ "XAO:0000054" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Rumpf", - "xrefs" : [ "BTO:0001493" ] - } ], + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "AAO:0010339" - }, { - "val" : "BILA:0000116" - }, { - "val" : "BTO:0001493" - }, { - "val" : "CALOHA:TS-1071" - }, { - "val" : "EFO:0000966" - }, { - "val" : "EMAPA:31857" - }, { - "val" : "FMA:7181" - }, { - "val" : "MA:0000004" - }, { - "val" : "MAT:0000296" - }, { - "val" : "MIAA:0000296" - }, { - "val" : "NCIT:C33816" - }, { - "val" : "SCTID:262225004" - }, { - "val" : "TAO:0001115" - }, { - "val" : "UMLS:C0460005" + "val" : "BILA:0000010" }, { - "val" : "Wikipedia:Torso" + "val" : "CARO:0001002" }, { - "val" : "XAO:0000054" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "XAO:0003025" + "val" : "FMA:24137" }, { - "val" : "ZFA:0001115" + "val" : "NCIT:C34022" }, { - "val" : "galen:Trunk" + "val" : "UMLS:C1515977" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24846,87 +27737,77 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002104", - "lbl" : "visual system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "lbl" : "cardiogenic splanchnic mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The sensory system subserving the sense of vision.", - "xrefs" : [ "NIFSTD:FMAID_7191" ] + "val" : "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. 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The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.", + "xrefs" : [ "Wikipedia:Rhombencephalon" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "SpC" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cerebro-cerebellar fissure", - "xrefs" : [ "NeuroNames:22" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cerebrocerebellar fissure", - "xrefs" : [ "NeuroNames:22" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "fissura cerebro-cerebellaris", - "xrefs" : [ "NeuroNames:22" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "fissura cerebrocerebellaris", - "xrefs" : [ "NeuroNames:22" ] + "pred" : "hasExactSynonym", + "val" : "presumptive rhombencephalon", + "xrefs" : [ "ZFA:0000569" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "medulla spinalis", - "xrefs" : [ "BTO:0001279", "Wikipedia:Spinal_cord" ] + "val" : "embryonic rhombencephalon", + "xrefs" : [ "CALOHA:TS-2118" ] }, { "pred" : "hasRelatedSynonym", - "val" : "spinal cord structure", - "xrefs" : [ "ZFA:0000075" ] + "val" : "future hindbrain", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "spinal medulla", - "xrefs" : [ "BTO:0001279" ] + "val" : "rhombencephalon", + "xrefs" : [ "EHDAA2:0001630" ] } ], "xrefs" : [ { - "val" : "AAO:0010151" - }, { - "val" : "BAMS:SP" - }, { - "val" : "BAMS:Spinal" - }, { - "val" : "BIRNLEX:1709" - }, { - "val" : "BM:SpC" - }, { - "val" : "BTO:0001279" - }, { - "val" : "CALOHA:TS-0953" - }, { - "val" : "DHBA:12890" - }, { - "val" : "DMBA:17651" - }, { - "val" : "EFO:0000110" - }, { - "val" : "EHDAA2:0001255" - }, { - "val" : "EHDAA:2863" - }, { - "val" : "EMAPA:17577" - }, { - "val" : "EV:0100316" - }, { - "val" : "FMA:7647" - }, { - "val" : "GAID:695" - }, { - "val" : "MA:0000216" - }, { - "val" : "MAT:0000183" - }, { - "val" : "MESH:D013116" - }, { - "val" : "MIAA:0000183" - }, { - "val" : "NCIT:C12464" - }, { - "val" : "SCTID:180959008" + "val" : "BAMS:HB" }, { - "val" : "TAO:0000075" + "val" : "CALOHA:TS-2118" }, { - "val" : "UMLS:C0037925" + "val" : "EFO:0003440" }, { - "val" : "VHOG:0000601" + "val" : "EHDAA2:0001630" }, { - "val" : "Wikipedia:Spinal_cord" + "val" : "FMA:295640" }, { - "val" : "XAO:0000020" + "val" : "TAO:0000569" }, { - "val" : "ZFA:0000075" + "val" : "Wikipedia:Rhombencephalon" }, { - "val" : "neuronames:22" + "val" : "ZFA:0000569" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - add superclass to unify with VNC?" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "TODO - unify naming conventions" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002298", - "lbl" : "brainstem", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007281", + "lbl" : "presumptive midbrain hindbrain boundary", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].", - "xrefs" : [ "ISBN:0471888893", "MP:0005277", "Wikipedia:Brainstem", "ZFA:0001707" ] + "val" : "Embryonic structure that gives rise to the midbrain hindbrain boundary.", + "xrefs" : [ "ZFA:0001187" ] }, - "comments" : [ "'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "brain stem", - "xrefs" : [ "ABA:BS" ] + "val" : "presumptive MHB", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "truncus encephali", - "xrefs" : [ "Wikipedia:Brainstem" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory medullary lamina of pallidum", - "xrefs" : [ "NeuroNames:236" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamella pallidi incompleta", - "xrefs" : [ "NeuroNames:236" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina medullaris accessoria", - "xrefs" : [ "NeuroNames:236" ] + "val" : "presumptive midbrain-hindbrain boundary", + "xrefs" : [ "ZFA:0001187" ] + } ], + "xrefs" : [ { + "val" : "EFO:0003446" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina medullaris incompleta pallidi", - "xrefs" : [ "NeuroNames:236" ] + "val" : "TAO:0001187" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina pallidi incompleta", - "xrefs" : [ "NeuroNames:236" ] + "val" : "XAO:0004086" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "val" : "ZFA:0001187" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007282", + "lbl" : "presumptive segmental plate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A presumptive structure that has the potential to develop into a presomitic mesoderm.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "truncus encephalicus", - "xrefs" : [ "BTO:0000146" ] + "val" : "presumptive segmental plates", + "xrefs" : [ "ZFA:0000053" ] } ], "xrefs" : [ { - "val" : "BAMS:BS" - }, { - "val" : "BIRNLEX:1565" - }, { - "val" : "BTO:0000146" - }, { - "val" : "CALOHA:TS-0093" - }, { - "val" : "EFO:0001962" - }, { - "val" : "EMAPA:32678" - }, { - "val" : "EV:0100241" - }, { - "val" : "FMA:79876" - }, { - "val" : "MA:0000169" - }, { - "val" : "MBA:343" - }, { - "val" : "MESH:D001933" - }, { - "val" : "NCIT:C12441" - }, { - "val" : "SCTID:180925009" - }, { - "val" : "TAO:0002156" - }, { - "val" : "UMLS:C0006121" - }, { - "val" : "VHOG:0001457" - }, { - "val" : "Wikipedia:Brainstem" + "val" : "EFO:0003421" }, { - "val" : "ZFA:0001707" + "val" : "TAO:0000053" }, { - "val" : "neuronames:236" + "val" : "ZFA:0000053" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002316", - "lbl" : "white matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007284", + "lbl" : "presumptive neural plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system.", - "xrefs" : [ "Wikipedia:White_matter", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A presumptive structure that has the potential to develop into a neural plate.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "CNS tract/commissure", - "xrefs" : [ "ZFA:0001682" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neuronal white matter", - "xrefs" : [ "AEO:0001011" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white matter of neuraxis", - "xrefs" : [ "FMA:83929" ] + "val" : "prospective neuroectoderm", + "xrefs" : [ "ZFA:0000063" ] }, { "pred" : "hasExactSynonym", - "val" : "white substance" - }, { - "pred" : "hasRelatedSynonym", - "val" : "CNS tracts and commissures", - "xrefs" : [ "TAO:0000145" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "CNS white matter", - "xrefs" : [ "TAO:0002143" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "substantia alba", - "xrefs" : [ "Wikipedia:White_matter" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "white mater", - "xrefs" : [ "VHOG:0001764" ] + "val" : "prospective vegetal ectoderm", + "xrefs" : [ "ZFA:0000063" ] } ], "xrefs" : [ { - "val" : "AEO:0000139" - }, { - "val" : "AEO:0001011" - }, { - "val" : "EMAPA:35927" - }, { - "val" : "FMA:83929" - }, { - "val" : "HBA:9218" - }, { - "val" : "MA:0001135" - }, { - "val" : "NCIT:C33892" - }, { - "val" : "NLX:412" - }, { - "val" : "NLXANAT:101177" - }, { - "val" : "PBA:294022044" - }, { - "val" : "TAO:0000145" + "val" : "EFO:0003424" }, { - "val" : "TAO:0002142" + "val" : "TAO:0000063" }, { - "val" : "TAO:0002143" + "val" : "ZFA:0000063" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging" }, { - "val" : "UMLS:C0682708" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007285", + "lbl" : "presumptive paraxial mesoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The part of the blastula that has the potential to develop into a paraxial mesoderm.", + "xrefs" : [ "UBERON:cjm", "https://github.com/obophenotype/uberon/issues/1277" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "future paraxial mesenchyme", + "xrefs" : [ "UBERON:cjm" ] }, { - "val" : "VHOG:0001764" + "pred" : "hasExactSynonym", + "val" : "future paraxial mesoderm" + } ], + "xrefs" : [ { + "val" : "EFO:0003443" }, { - "val" : "Wikipedia:White_matter" + "val" : "TAO:0000591" }, { - "val" : "ZFA:0001682" + "val" : "XAO:0004134" }, { - "val" : "neuronames:2870" + "val" : "ZFA:0000591" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", - "lbl" : "coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007418", + "lbl" : "neural decussation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.", - "xrefs" : [ "BTO:0001707" ] + "val" : "Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6).", + "xrefs" : [ "NLX:144064" ] }, - "comments" : [ "EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo" ], "synonyms" : [ { "pred" : "hasBroadSynonym", - "val" : "body cavity", - "xrefs" : [ "BTO:0001707" ] + "val" : "chiasm" }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity", - "xrefs" : [ "EHDAA2:0000267" ] + "pred" : "hasBroadSynonym", + "val" : "chiasma" }, { - "pred" : "hasExactSynonym", - "val" : "coelomic cavity lumen", - "xrefs" : [ "EHDAA2:0000267" ] + "pred" : "hasBroadSynonym", + "val" : "decussation" }, { "pred" : "hasExactSynonym", - "val" : "main body cavity" + "val" : "decussation of neuraxis", + "xrefs" : [ "FMA:83858" ] }, { "pred" : "hasExactSynonym", - "val" : "space of body compartment", - "xrefs" : [ "FMA:85006" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "ventral body cavity", - "xrefs" : [ "NCBITaxon:7742" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "celom", - "xrefs" : [ "BTO:0001707" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "coelom" + "val" : "neuraxis chiasm" }, { - "pred" : "hasRelatedSynonym", - "val" : "coelome", - "xrefs" : [ "BTO:0001707" ] + "pred" : "hasExactSynonym", + "val" : "neuraxis chiasma" }, { - "pred" : "hasRelatedSynonym", - "val" : "hemocoel", - "xrefs" : [ "FBbt:00005060" ] + "pred" : "hasExactSynonym", + "val" : "neuraxis decussation", + "xrefs" : [ "FMA:83858" ] } ], "xrefs" : [ { - "val" : "AEO:0000186" - }, { - "val" : "BTO:0001707" - }, { - "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" - }, { - "val" : "FMA:85006" - }, { - "val" : "NCIT:C25444" - }, { - "val" : "RETIRED_EHDAA2:0003186" - }, { - "val" : "SCTID:361348008" - }, { - "val" : "TAO:0001438" + "val" : "FMA:83858" }, { - "val" : "UMLS:C0333343" + "val" : "NCIT:C28351" }, { - "val" : "ZFA:0001438" + "val" : "NLX:144064" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007425", + "lbl" : "decussation of diencephalon", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A neural decussation that is part of a diencephalon.", + "xrefs" : [ "OBOL:automatic" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "diencephalon decussation", + "xrefs" : [ "FMA:62446" ] + } ], + "xrefs" : [ { + "val" : "FMA:62446" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007500", + "lbl" : "epithelial tube open at both ends", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelial tube open at both ends that allows fluid flow.", + "xrefs" : [ "AEO:JB", "UBERONREF:0000001" ] + }, + "xrefs" : [ { + "val" : "AEO_RETIRED:0000116" }, { - "val" : "galen:BodyCavity" + "val" : "RETIRED_EHDAA2:0003116" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0000169" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "lbl" : "notochord", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007503", + "lbl" : "epithelial vesicle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A flexible rod-shaped body found in embryos of all chordates. 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In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" + "pred" : "hasBroadSynonym", + "val" : "field" }, { "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] + "val" : "developmental field" }, { - "pred" : "hasExactSynonym", - "val" : "textus muscularis" + "pred" : "hasRelatedSynonym", + "val" : "future organ" + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ field" } ], "xrefs" : [ { - "val" : "AAO:0000306" - }, { - "val" : "AEO:0000122" - }, { - "val" : "CALOHA:TS-0642" - }, { - "val" : "EHDAA2:0003122" - }, { - "val" : "EMAPA:32715" - }, { - "val" : "FMA:9641" - }, { - "val" : "MA:0002437" - }, { - "val" : "MESH:D009132" - }, { - "val" : "NCIT:C12435" + "val" : "AEO:0000170" }, { - "val" : "SCTID:91727004" + "val" : "EFO:0001649" }, { - "val" : "UMLS:C2328219" + "val" : "EHDAA2:0003170" }, { - "val" : "Wikipedia:Muscle_tissue" + "val" : "FBbt:00005426" }, { - "val" : "galen:MuscleTissue" + "val" : "Wikipedia:Anlage_(biology)" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -25997,142 +28405,63 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007702", + "lbl" : "tract of brain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "An axon tract that is part of a brain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "haematological system" - }, { - "pred" : "hasExactSynonym", - "val" : "haemopoietic system" - }, { - "pred" : "hasExactSynonym", - "val" : "organa haemopoietica" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Blutbildungssystem", - "xrefs" : [ "BTO:0000570" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "haematopoietic system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematological system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematolymphoid system" + "val" : "brain tract", + "xrefs" : [ "FMA:83848" ] }, { "pred" : "hasRelatedSynonym", - "val" : "hemopoietic system" + "val" : "landmark tracts", + "xrefs" : [ "DMBA:tracts" ] } ], "xrefs" : [ { - "val" : "AAO:0011002" - }, { - "val" : "BTO:0000570" - }, { - "val" : "CALOHA:TS-0449" - }, { - "val" : "EFO:0000798" - }, { - "val" : "EMAPA:35402" - }, { - "val" : "EV:0100045" - }, { - "val" : "FMA:9667" - }, { - "val" : "GAID:1008" - }, { - "val" : "MA:0002434" - }, { - "val" : "MAT:0000022" - }, { - "val" : "MESH:D006413" - }, { - "val" : "MIAA:0000022" - }, { - "val" : "NCIT:C12909" - }, { - "val" : "SCTID:362587009" - }, { - "val" : "TAO:0005023" - }, { - "val" : "UMLS:C0018957" - }, { - "val" : "VHOG:0001624" - }, { - "val" : "Wikipedia:Haematopoiesis" - }, { - "val" : "XAO:0000122" - }, { - "val" : "ZFA:0005023" + "val" : "FMA:83848" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002506", - "lbl" : "iris epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007798", + "lbl" : "vascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelium that is part of a iris [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Anatomical system that consists of all blood and lymph vessels.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial tissue of iris", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of iris", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium pigmentosum (iris)", - "xrefs" : [ "FMA:58517" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "epithelium pigmentosum iridis", - "xrefs" : [ "FMA:58517", "FMA:TA" ] + "xrefs" : [ { + "val" : "BTO:0001085" }, { - "pred" : "hasExactSynonym", - "val" : "iris epithelial tissue", - "xrefs" : [ "OBOL:automatic" ] + "val" : "CALOHA:TS-2053" }, { - "pred" : "hasExactSynonym", - "val" : "iris epithelium", - "xrefs" : [ "FMA:58517" ] + "val" : "EHDAA2:0004520" }, { - "pred" : "hasExactSynonym", - "val" : "pigmented epithelium of iris", - "xrefs" : [ "FMA:58517" ] + "val" : "EMAPA:35905" }, { - "pred" : "hasRelatedSynonym", - "val" : "iris pigmented epithelium", - "xrefs" : [ "MA:0002826" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35447" + "val" : "MA:0002718" }, { - "val" : "FMA:58517" + "val" : "NCIT:C33854" }, { - "val" : "MA:0002826" + "val" : "UMLS:C0489903" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with vasculature" + }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -26141,134 +28470,105 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", - "lbl" : "epiblast (generic)", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007811", + "lbl" : "craniocervical region", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", - "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] + "val" : "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epiblast", - "xrefs" : [ "VHOG:0000243" ] + "pred" : "hasRelatedSynonym", + "val" : "cephalic area", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] }, { "pred" : "hasRelatedSynonym", - "val" : "blastocyst" + "val" : "cephalic part of animal", + "xrefs" : [ "Wikipedia:Head" ] }, { "pred" : "hasRelatedSynonym", - "val" : "ectoblast", - "xrefs" : [ "MP:0003886" ] + "val" : "cephalic region", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "epiblastus", - "xrefs" : [ "Wikipedia:Epiblast" ] + "val" : "head and neck", + "xrefs" : [ "FMA:280881" ] }, { "pred" : "hasRelatedSynonym", - "val" : "primitive ectoderm", - "xrefs" : [ "VHOG:0000243" ] + "val" : "head or neck" } ], "xrefs" : [ { - "val" : "BTO:0004593" + "val" : "CALOHA:TS-2356" }, { - "val" : "FMA:296704" + "val" : "EV:0100009" }, { - "val" : "MAT:0000067" + "val" : "FMA:280881" }, { - "val" : "MIAA:0000067" + "val" : "MA:0000006" }, { - "val" : "VHOG:0000243" + "val" : "NCIT:C12418" }, { - "val" : "Wikipedia:Epiblast" + "val" : "SCTID:361355005" + }, { + "val" : "UMLS:C0460004" + }, { + "val" : "WikipediaCategory:Head_and_neck" + }, { + "val" : "galen:HeadAndNeck" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002546", - "lbl" : "cranial placode", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", + "lbl" : "entire embryonic mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.", - "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK53175/", "https://github.com/obophenotype/uberon/issues/135", "https://github.com/seger/aao/issues/4", "https://orcid.org/0000-0002-6601-2165", "https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/" ] + "val" : "Sum total of mesenchyme in the embryo.", + "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", - "pred" : "hasBroadSynonym", - "val" : "ectodermal placode", - "xrefs" : [ "FMA:293966", "PMID:22512454" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "placode", - "xrefs" : [ "Wikipedia:Placode" ] - }, { - "pred" : "hasExactSynonym", - "val" : "ectodermal cranial placode", - "xrefs" : [ "UBERON:cjm" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "cranial placodes", - "xrefs" : [ "XAO:0000305" ] - } ], "xrefs" : [ { - "val" : "AAO:0010466" - }, { - "val" : "EFO:0001650" - }, { - "val" : "MAT:0000369" + "val" : "EHDAA2:0001113" }, { - "val" : "MIAA:0000369" + "val" : "EHDAA:177" }, { - "val" : "XAO:0000305" + "val" : "EMAPA:16097" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Do not merge with neurogenic placode" + "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", + "lbl" : "subdivision of trunk", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" + "pred" : "hasExactSynonym", + "val" : "region of trunk", + "xrefs" : [ "FMA:25054" ] + }, { + "pred" : "hasExactSynonym", + "val" : "trunk subdivision", + "xrefs" : [ "FMA:25054" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" - }, { - "val" : "NCIT:C34007" + "val" : "FMA:25054" }, { - "val" : "galen:Cavity" + "val" : "SCTID:22943007" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26276,154 +28576,127 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002616", - "lbl" : "regional part of brain", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009581", + "lbl" : "midbrain mantle layer", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.", - "xrefs" : [ "BIRNLEX:1167" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "anatomical structure of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "biological structure of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "brain anatomical structure", - "xrefs" : [ "OBOL:automatic" ] + "val" : "mantle layer lateral wall midbrain", + "xrefs" : [ "VHOG:0000910" ] }, { "pred" : "hasExactSynonym", - "val" : "brain biological structure", - "xrefs" : [ "OBOL:automatic" ] + "val" : "midbrain lateral wall mantle layer" }, { - "pred" : "hasExactSynonym", - "val" : "brain part" + "pred" : "hasRelatedSynonym", + "val" : "mantle layer lateral wall mesencephalon", + "xrefs" : [ "VHOG:0000910" ] + } ], + "xrefs" : [ { + "val" : "EHDAA2:0001172" }, { - "pred" : "hasExactSynonym", - "val" : "neuraxis segment", - "xrefs" : [ "FMA:55676" ] + "val" : "EMAPA:16977" }, { + "val" : "VHOG:0000910" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009615", + "lbl" : "midbrain hindbrain boundary neural plate", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neuroanatomical region" + "val" : "MHB neural plate", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "segment of brain", - "xrefs" : [ "BIRNLEX:1167" ] + "val" : "midbrain-hindbrain boundary neural plate", + "xrefs" : [ "ZFA:0007044" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1167" - }, { - "val" : "FMA:55676" - }, { - "val" : "NCIT:C13031" - }, { - "val" : "SCTID:384763002" + "val" : "TAO:0007044" }, { - "val" : "UMLS:C0445620" + "val" : "ZFA:0007044" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - developmental relationships for lines" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003052", - "lbl" : "midbrain-hindbrain boundary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009616", + "lbl" : "presumptive midbrain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.", - "xrefs" : [ "GO:0021555" ] + "val" : "A presumptive structure that has the potential to develop into a midbrain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "MHB" - }, { - "pred" : "hasExactSynonym", - "val" : "mid-hindbrain boundary" - }, { - "pred" : "hasExactSynonym", - "val" : "mid-hindbrain junction" - }, { - "pred" : "hasExactSynonym", - "val" : "midbrain hindbrain boundary" - }, { - "pred" : "hasRelatedSynonym", - "val" : "isthmic organizer territory", - "xrefs" : [ "XAO:0000016" ] + "val" : "presumptive mesencephalon", + "xrefs" : [ "ZFA:0000148" ] }, { "pred" : "hasRelatedSynonym", - "val" : "isthmo-cerebellar region", - "xrefs" : [ "VHOG:0000649" ] + "val" : "early midbrain", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "isthmus" + "val" : "future midbrain", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "isthmus/MHB", - "xrefs" : [ "Geisha:syn", "NCBITaxon:8782" ] + "val" : "mesencephalon", + "xrefs" : [ "EHDAA2:0000615" ] } ], "xrefs" : [ { - "val" : "AAO:0011064" - }, { - "val" : "DMBA:16810" - }, { - "val" : "EHDAA2:0004395" - }, { - "val" : "EHDAA:5789" - }, { - "val" : "EMAPA:32857" + "val" : "BAMS:MES" }, { - "val" : "NCIT:C93172" + "val" : "EFO:0003432" }, { - "val" : "TAO:0000042" + "val" : "EHDAA2:0000615" }, { - "val" : "VHOG:0000649" + "val" : "EMAPA:16140" }, { - "val" : "XAO:0000016" + "val" : "TAO:0000148" }, { - "val" : "ZFA:0000042" + "val" : "Wikipedia:Mesencephalon" }, { - "val" : "neuronames:2076" + "val" : "ZFA:0000148" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding class for organizer. Consider adding separate class for isthmus as a structure" + "val" : "TODO - unify naming conventions" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003056", - "lbl" : "pre-chordal neural plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", + "lbl" : "trunk paraxial mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "The portion of neural plate anterior to the mid-hindbrain junction.", - "xrefs" : [ "XB:curator" ] - }, "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "trunk and cervical paraxial mesenchyme", + "xrefs" : [ "EHDAA2:0002094" ] + }, { "pred" : "hasRelatedSynonym", - "val" : "anterior neural plate" + "val" : "trunk paraxial mesenchyme", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] } ], "xrefs" : [ { - "val" : "AAO:0011084" - }, { - "val" : "TAO:0007016" - }, { - "val" : "VHOG:0001200" - }, { - "val" : "XAO:0000045" - }, { - "val" : "ZFA:0007016" + "val" : "EHDAA2:0002094" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26431,26 +28704,22 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003057", - "lbl" : "chordal neural plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "lbl" : "anterior lateral plate mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "The portion of neural plate posterior to the mid-hindbrain junction.", - "xrefs" : [ "XB:curator" ] - }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "posterior neural plate" + "pred" : "hasExactSynonym", + "val" : "ALPM", + "xrefs" : [ "ZFA:0005041" ] } ], "xrefs" : [ { - "val" : "TAO:0007017" - }, { - "val" : "VHOG:0001201" + "val" : "EFO:0003704" }, { - "val" : "XAO:0000046" + "val" : "TAO:0005041" }, { - "val" : "ZFA:0007017" + "val" : "ZFA:0005041" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26458,56 +28727,40 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009891", + "lbl" : "facial mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "Mesenchyme that is part of a developing face.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segmental plate" + "val" : "face mesenchyme" }, { "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] + "val" : "mesenchyme of face" } ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" + "val" : "EMAPA:35337" }, { - "val" : "XAO:0000057" + "val" : "FMA:302884" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009920", + "lbl" : "optic neural crest", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EHDAA2:0001315" }, { - "val" : "ZFA:0000279" + "val" : "EHDAA:1122" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26515,219 +28768,150 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", - "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ventral lateral plate mesoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "blood islands" - }, { - "pred" : "hasRelatedSynonym", - "val" : "VBI" - }, { - "pred" : "hasRelatedSynonym", - "val" : "caudal hematopoietic tissue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior ICM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior blood island" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral blood island" + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { - "val" : "AAO:0011006" - }, { - "val" : "EFO:0003489" - }, { - "val" : "EHDAA:207" - }, { - "val" : "NCIT:C34113" - }, { - "val" : "TAO:0000094" - }, { - "val" : "TE:E5.11.2.0.0.0.4" - }, { - "val" : "UMLS:C1511224" + "val" : "CARO:0010000" }, { - "val" : "VHOG:0000085" + "val" : "FBbt:00100313" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "Wikipedia:Blood_island_of_umbilical_vesicle" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "XAO:0000067" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "ZFA:0000094" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "lbl" : "axial mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010096", + "lbl" : "future myelencephalon", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.", - "xrefs" : [ "GO:0048318", "Wikipedia:Chordamesoderm" ] + "val" : "A developing anatomical structure that has the potential to develop into a myelencephalon.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm", - "xrefs" : [ "Wikipedia:Chordamesoderm" ] - } ], "xrefs" : [ { - "val" : "AAO:0011017" - }, { - "val" : "EFO:0003647" - }, { - "val" : "TAO:0001204" - }, { - "val" : "VHOG:0000107" - }, { - "val" : "Wikipedia:Chordamesoderm" - }, { - "val" : "XAO:0000205" - }, { - "val" : "ZFA:0001204" + "val" : "EHDAA2:0000640" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010199", + "lbl" : "bona-fide anatomical boundary", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical boundary that corresponds to some physical discontinuity.", + "xrefs" : [ "CARO:0001004" ] + }, + "comments" : [ "One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "CARO:0001004" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003071", - "lbl" : "eye primordium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010230", + "lbl" : "eyeball of camera-type eye", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. 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Excludes joints.", + "xrefs" : [ "UBERONREF:0000003", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cardiac field", - "xrefs" : [ "ZFA:0000028" ] + "pred" : "hasExactSynonym", + "val" : "skeletal subdivision", + "xrefs" : [ "VSAO:0000042" ] }, { "pred" : "hasRelatedSynonym", - "val" : "fused heart primordium" + "val" : "subdivision of skeleton (in vivo)", + "xrefs" : [ "FMA:23879" ] } ], "xrefs" : [ { - "val" : "AAO:0011044" - }, { - "val" : "BTO:0001887" - }, { - "val" : "NCIT:C34276" - }, { - "val" : "TAO:0000028" - }, { - "val" : "UMLS:C1514450" + "val" : "FMA:23879" }, { - "val" : "XAO:0000336" + "val" : "SCTID:129140006" }, { - "val" : "ZFA:0000028" + "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "should probably be merged with heart rudiment." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "lbl" : "sclerotome", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011137", + "lbl" : "axial skeletal system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].", - "xrefs" : [ "Wikipedia:Sclerotome", "XB:curator", "https://github.com/obophenotype/uberon/issues/316" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "sclerotomes", - "xrefs" : [ "TAO:0001080" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "sclerotomus", - "xrefs" : [ "Wikipedia:Sclerotome" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010571" - }, { - "val" : "AEO:0000212" - }, { - "val" : "EHDAA2:0003439" - }, { - "val" : "EMAPA:31159" - }, { - "val" : "FMA:295652" - }, { - "val" : "NCIT:C34287" - }, { - "val" : "TAO:0001080" - }, { - "val" : "UMLS:C0183176" - }, { - "val" : "VHOG:0000680" - }, { - "val" : "Wikipedia:Sclerotome" - }, { - "val" : "XAO:0000397" - }, { - "val" : "ZFA:0001080" + "val" : "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "xrefs" : [ { + "val" : "FMA:7483" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003098", - "lbl" : "optic stalk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011138", + "lbl" : "postcranial axial skeletal system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain.", - "xrefs" : [ "ISBN:0-914294-08-3", "MP:0004268" ] + "val" : "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/44", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "optic stalks", - "xrefs" : [ "ZFA:0000137" ] + "pred" : "hasBroadSynonym", + "val" : "axial skeletal system", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "pedunculus opticus", - "xrefs" : [ "Wikipedia:Optic_stalk" ] + "pred" : "hasExactSynonym", + "val" : "post-cranial axial skeletal system" } ], "xrefs" : [ { - "val" : "AAO:0011077" - }, { - "val" : "EHDAA2:0001318" - }, { - "val" : "EHDAA:3816" - }, { - "val" : "EMAPA:16678" - }, { - "val" : "NCIT:C34235" - }, { - "val" : "SCTID:308788004" - }, { - "val" : "TAO:0000137" - }, { - "val" : "UMLS:C0231107" - }, { - "val" : "VHOG:0000223" - }, { - "val" : "Wikipedia:Optic_stalk" - }, { - "val" : "XAO:0000475" - }, { - "val" : "ZFA:0000137" + "val" : "FMA:302077" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003099", - "lbl" : "cranial neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011215", + "lbl" : "central nervous system cell part cluster", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.", - "xrefs" : [ "MGI:anna" ] + "val" : "A multi cell part structure that is part of a central nervous system.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "CNC", - "xrefs" : [ "XAO:0001001" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cephalic neural crest", - "xrefs" : [ "EMAPA:16091" ] - }, { "pred" : "hasExactSynonym", - "val" : "cranial NCC population" + "val" : "cell part cluster of neuraxis", + "xrefs" : [ "FMA:83143" ] }, { "pred" : "hasExactSynonym", - "val" : "head NCC population" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "crista neuralis cranialis", - "xrefs" : [ "Wikipedia:Cranial_neural_crest" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "head crest" - }, { - "pred" : "hasRelatedSynonym", - "val" : "head neural crest" + "val" : "neuraxis layer", + "xrefs" : [ "FMA:83143" ] } ], "xrefs" : [ { - "val" : "AAO:0010580" - }, { - "val" : "EFO:0003645" - }, { - "val" : "EHDAA2:0004420" - }, { - "val" : "EMAPA:16091" - }, { - "val" : "TAO:0001194" - }, { - "val" : "VHOG:0000063" - }, { - "val" : "Wikipedia:Cranial_neural_crest" - }, { - "val" : "XAO:0001001" - }, { - "val" : "ZFA:0001194" + "val" : "FMA:83143" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27237,275 +29225,161 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", - "lbl" : "compound organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011216", + "lbl" : "organ system subdivision", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", - "xrefs" : [ "CARO:0000024" ] + "val" : "A subdivision of an anatomical system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "organ" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "AAO:0010015" - }, { - "val" : "AEO:0000024" - }, { - "val" : "BILA:0000024" - }, { - "val" : "CARO:0000024" - }, { - "val" : "EHDAA2:0003024" - }, { - "val" : "HAO:0000024" + "val" : "FBbt:00007330" }, { - "val" : "TADS:0000598" + "val" : "FMA:67509" }, { - "val" : "TAO:0000496" + "val" : "SCTID:91690000" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "val" : "TGMA:0001837" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "val" : "VHOG:0001723" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { - "val" : "XAO:0003041" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "ZFA:0000496" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "lbl" : "mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011222", + "lbl" : "intra-ocular muscle", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.", - "xrefs" : [ "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up", "https://en.wikipedia.org/wiki/Mesenchyme", "https://github.com/obophenotype/uberon/issues/1641" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "mesenchymal tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "mesenchyme tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of mesenchymal tissue" + "val" : "intrinsic muscle of eyeball" }, { "pred" : "hasExactSynonym", - "val" : "portion of mesenchyme tissue" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesenchyma", - "xrefs" : [ "Wikipedia:Mesenchyme" ] + "val" : "intrinsic ocular muscle", + "xrefs" : [ "EMAPA:18808" ] } ], "xrefs" : [ { - "val" : "AAO:0010427" - }, { - "val" : "AEO:0000145" - }, { - "val" : "BTO:0001393" - }, { - "val" : "CALOHA:TS-0620" - }, { - "val" : "EHDAA2:0003145" - }, { - "val" : "EV:0100007" - }, { - "val" : "NCIT:C13301" - }, { - "val" : "TAO:0000393" - }, { - "val" : "UMLS:C0162415" - }, { - "val" : "VHOG:0000170" - }, { - "val" : "Wikipedia:Mesenchyme" + "val" : "AAO:0010038" }, { - "val" : "XAO:0003046" + "val" : "EMAPA:18808" }, { - "val" : "ZFA:0000393" + "val" : "FMA:49150" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003314", - "lbl" : "eye mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011585", + "lbl" : "cell condensation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Mesenchyme that is part of a developing camera-type eye.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000006", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of eye", - "xrefs" : [ "OBOL:automatic" ] - } ], "xrefs" : [ { - "val" : "EHDAA2:0000485" - }, { - "val" : "EHDAA:2910" - }, { - "val" : "EMAPA:16673" + "val" : "VSAO:0000006" }, { - "val" : "VHOG:0001084" + "val" : "XAO:0004021" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - change mesenchyme relationships to precursor_of" + "val" : "consider obsoleting, coordinate with VSAO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003386", - "lbl" : "smooth muscle of eye", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011591", + "lbl" : "tract of diencephalon", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi.", - "xrefs" : [ "MGI:cwg", "MP:0005247" ] + "val" : "An axon tract that is part of a diencephalon.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "ocular smooth muscle", - "xrefs" : [ "MA:0001268" ] + "val" : "diencephalon tract", + "xrefs" : [ "FMA:62447" ] } ], "xrefs" : [ { - "val" : "EMAPA:18807" - }, { - "val" : "MA:0001268" + "val" : "FMA:62447" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003544", - "lbl" : "brain white matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011676", + "lbl" : "subdivision of organism along main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites.", - "xrefs" : [ "MP:0008026" ] + "val" : "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "brain white matter of neuraxis", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "brain white substance", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white matter of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white matter of neuraxis of brain", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "white substance of brain", - "xrefs" : [ "OBOL:automatic" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35187" - }, { - "val" : "MA:0000820" + "val" : "axial subdivision of organism" }, { - "val" : "NCIT:C49334" + "pred" : "hasRelatedSynonym", + "val" : "body segment" }, { - "val" : "UMLS:C1706995" + "pred" : "hasRelatedSynonym", + "val" : "main body segment" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003566", - "lbl" : "head connective tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", + "lbl" : "embryonic cardiovascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A portion of connective tissue that is part of a head [Automatically generated definition].", + "val" : "A cardiovascular system that is part of a conceptus.", "xrefs" : [ "OBOL:automatic" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "adult head connective tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "adult head portion of connective tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "adult head textus connectivus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "connective tissue of adult head", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "connective tissue of head", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "head portion of connective tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "head textus connectivus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue of adult head", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue of head", - "xrefs" : [ "OBOL:automatic" ] + "val" : "conceptus cardiovascular system" }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus of adult head", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "embryonic circulatory system" }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus of head", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "fetal circulatory system" } ], "xrefs" : [ { - "val" : "MA:0000577" + "val" : "EHDAA2:0000216" + }, { + "val" : "FMA:305965" + }, { + "val" : "NCIT:C34148" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27513,141 +29387,64 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003714", - "lbl" : "neural tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011814", + "lbl" : "non-neurogenic ectodermal placode", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.", - "xrefs" : [ "FMA:9642" ] + "val" : "Ectodermal placode that does not develop into a component of the nervous system.", + "xrefs" : [ "PMID:11523831", "http://orcid.org/0000-0002-6601-2165" ] }, - 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"xrefs" : [ "OBOL:automatic" ] + "val" : "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.", + "xrefs" : [ "FMA:20107" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cavity of neural tube", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "lumen of neural tube", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neural tube neural lumen", - "xrefs" : [ "EHDAA2:0001269" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "prosencoel" - }, { - "pred" : "hasRelatedSynonym", - "val" : "central lumen" - }, { - "pred" : "hasRelatedSynonym", - "val" : "neural lumen", - "xrefs" : [ "EHDAA:2889" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neurocoel", - "xrefs" : [ "VHOG:0001119" ] - } ], "xrefs" : [ { - "val" : "AAO:0011073" - }, { - "val" : "EHDAA2:0001269" - }, { - "val" : "EHDAA:2889" - }, { - "val" : "EHDAA:914" - }, { - "val" : "EMAPA:16167" - }, { - "val" : "VHOG:0001119" - }, { - "val" : "XAO:0000252" + "val" : "FMA:20107" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005713" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003849", - "lbl" : "mesencephalic neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011825", + "lbl" : "loose connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a midbrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.", + "xrefs" : [ "FMA:19783" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "mesencephalic neural crest", - "xrefs" : [ "ZFA:0000935" ] + "val" : "textus connectivus collagenosus laxus", + "xrefs" : [ "FMA:19783", "FMA:TA" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "neural crest midbrain", - "xrefs" : [ "ZFA:0000935" ] + "val" : "textus connectivus laxus", + "xrefs" : [ "FMA:19783", "FMA:TA" ] } ], "xrefs" : [ { - "val" : "EFO:0003591" - }, { - "val" : "EHDAA2:0001101" - }, { - "val" : "EHDAA:360" + "val" : "FMA:19783" }, { - "val" : "TAO:0000935" + "val" : "NCIT:C33007" }, { - "val" : "VHOG:0000796" + "val" : "UMLS:C1253917" }, { - "val" : "ZFA:0000935" + "val" : "Wikipedia:Loose_connective_tissue" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27655,44 +29452,50 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003851", - "lbl" : "diencephalon neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011892", + "lbl" : "anterior uvea", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a diencephalon.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.", + "xrefs" : [ "MP:0005194" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "diencephalic neural crest", - "xrefs" : [ "ZFA:0000811" ] + "val" : "Haller tunica vascula", + "xrefs" : [ "MP:0005194" ] }, { "pred" : "hasExactSynonym", - "val" : "future diencephalon neural crest", - "xrefs" : [ "EHDAA2:0000603" ] + "val" : "anterior part of uveal tract" }, { "pred" : "hasExactSynonym", - "val" : "neural crest diencephalon", - "xrefs" : [ "ZFA:0000811" ] + "val" : "anterior uveal tract" }, { "pred" : "hasExactSynonym", - "val" : "neural crest of future diencephalon", - "xrefs" : [ "EMAPA:16518" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003573" + "val" : "anterior vascular layer of the eyeball" }, { - "val" : "EHDAA2:0000603" + "pred" : "hasExactSynonym", + "val" : "anterior vascular tunic of the eye" + }, { + "pred" : "hasExactSynonym", + "val" : "tunica vasculosa bulbosa", + "xrefs" : [ "MP:0005194" ] }, { - "val" : "EMAPA:16518" + "pred" : "hasExactSynonym", + "val" : "ventral uveal tract" }, { - "val" : "TAO:0000811" + "pred" : "hasRelatedSynonym", + "val" : "ciliary body and iris" }, { - "val" : "VHOG:0000798" + "pred" : "hasRelatedSynonym", + "val" : "vasculosa oculi", + "xrefs" : [ "MP:0005194" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37417" }, { - "val" : "ZFA:0000811" + "val" : "SCTID:280656002" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27700,72 +29503,66 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003852", - "lbl" : "rhombencephalon neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", + "lbl" : "coelom", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural crest hindbrain", - "xrefs" : [ "ZFA:0007063" ] + "pred" : "hasNarrowSynonym", + "val" : "enterocoelom", + "xrefs" : [ "NCBITaxon:33511" ] }, { - "pred" : "hasExactSynonym", - "val" : "rhombencephalic neural crest", - "xrefs" : [ "ZFA:0007063" ] + "pred" : "hasNarrowSynonym", + "val" : "haemocoelom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "schizocoelom" }, { "pred" : "hasRelatedSynonym", - "val" : "rhombomere neural crest", - "xrefs" : [ "EMAPA:35747" ] + "val" : "coelem" + }, { + "pred" : "hasRelatedSynonym", + "val" : "coelomic cavity", + "xrefs" : [ "EHDAA2:0004731" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0001628" - }, { - "val" : "EHDAA:362" - }, { - "val" : "EMAPA:35747" - }, { - "val" : "TAO:0007063" - }, { - "val" : "VHOG:0001210" + "val" : "EHDAA2:0004731" }, { - "val" : "ZFA:0007063" + "val" : "Wikipedia:Coelom" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003853", - "lbl" : "spinal cord neural crest", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", + "lbl" : "meso-epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.", + "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", "xrefs" : [ "OBOL:automatic" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neural crest spinal cord", - "xrefs" : [ "VHOG:0001006" ] + "val" : "mesoderm-derived epithelium" }, { - "pred" : "hasRelatedSynonym", - "val" : "spinal neural crest", - "xrefs" : [ "VHOG:0001006" ] + "pred" : "hasExactSynonym", + "val" : "mesoepithelium" } ], "xrefs" : [ { - "val" : "EHDAA:696" - }, { - "val" : "EMAPA:16163" - }, { - "val" : "EMAPA:16881" - }, { - "val" : "VHOG:0001006" + "val" : "FMA:86452" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27773,256 +29570,176 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "lbl" : "future coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012430", + "lbl" : "tunica fibrosa of eyeball", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.", + "xrefs" : [ "Wikipedia:Fibrous_tunic_of_eyeball" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "tunica fibrosa" + }, { "pred" : "hasExactSynonym", - "val" : "future coelomic cavity lumen" + "val" : "fibrous layer of eyeball", + "xrefs" : [ "FMA:58102" ] }, { "pred" : "hasRelatedSynonym", - "val" : "body cavity precursor" + "val" : "corneosclera", + "xrefs" : [ "Wikipedia:Fibrous_tunic_of_eyeball" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "fibrous tunic", + "xrefs" : [ "Wikipedia:Fibrous_tunic_of_eyeball" ] + } ], + "xrefs" : [ { + "val" : "FMA:58102" + }, { + "val" : "SCTID:361318005" + }, { + "val" : "Wikipedia:Fibrous_tunic_of_eyeball" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", - "lbl" : "intraembryonic coelom", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012467", + "lbl" : "enclosed anatomical space", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", - "xrefs" : [ "MGI:anna", "MP:0012187" ] + "val" : "An anatomical space with no opening to another space or to the exterior.", + "xrefs" : [ "AEO:0000222" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "somatic coelom", - "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] + "val" : "closed anatomical space" } ], "xrefs" : [ { - "val" : "EHDAA:251" - }, { - "val" : "EMAPA:16088" - }, { - "val" : "NCIT:C34195" - }, { - "val" : "UMLS:C1512940" - }, { - "val" : "VHOG:0000316" - }, { - "val" : "Wikipedia:Intraembryonic_coelom" + "val" : "AEO:0000222" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "lbl" : "stroma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", + "lbl" : "subdivision of tube", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Connective, non-functional supportive framework of a biological cell, tissue, or organ. 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"id" : "http://purl.obolibrary.org/obo/UBERON_0003914", - "lbl" : "epithelial tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", + "lbl" : "main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", - "xrefs" : [ "GO:0060562", "PMID:12526790" ] + "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial or endothelial tube" - } ], - "xrefs" : [ { - "val" : "AEO:0000114" - }, { - "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003931", - "lbl" : "diencephalic white matter", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", + "lbl" : "body proper", "type" : "CLASS", "meta" : { "definition" : { - "val" : "White matter that is part of a diencephalon [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The region of the organism associated with the visceral organs.", + "xrefs" : [ "AEO:0000103" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "diencephalic tract/commissure", - "xrefs" : [ "ZFA:0000338" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "diencephalic tracts and commissures", - "xrefs" : [ "TAO:0000338" ] - }, { - "pred" : "hasExactSynonym", - "val" : "predominantly white regional part of diencephalon", - "xrefs" : [ "BIRNLEX:1678" ] + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103" ] }, { - "pred" : "hasExactSynonym", - "val" : "white matter of diencephalon", - "xrefs" : [ "FMA:83931" ] + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1678" - }, { - "val" : "FMA:83931" + "val" : "AEO:0000103" }, { - "val" : "TAO:0000338" + "val" : "BTO:0001489" }, { - "val" : "ZFA:0000338" + "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0023148" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004022", - "lbl" : "germinal neuroepithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "lbl" : "mesenchyme derived from neural crest", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells.", - "xrefs" : [ "MP:0004261", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "Mesenchyme that develops_from the neural crest[Automatically generated definition].", + "xrefs" : [ "OBOL:automatic", "https://github.com/obophenotype/uberon/issues/248" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "germinal neuroepithelial layer", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "mesenchyme from neural crest" }, { "pred" : "hasExactSynonym", - "val" : "germinal neuroepithelium", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "neural crest derived mesenchyme" }, { "pred" : "hasExactSynonym", - "val" : "original neural tube", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "neural crest mesenchyme" + } ], + "xrefs" : [ { + "val" : "EMAPA:32735" + }, { + "val" : "FMA:293883" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28030,78 +29747,56 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004060", - "lbl" : "neural tube ventricular layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", + "lbl" : "thoracic skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.", - "xrefs" : [ "MP:0009689", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", + "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ependymal layer", - "xrefs" : [ "NCBIBook:NBK10047" ] - }, { "pred" : "hasExactSynonym", - "val" : "neural tube ependymal layer", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "skeleton of thorax" }, { "pred" : "hasExactSynonym", - "val" : "neural tube ventricular germinal zone", - "xrefs" : [ "NCBIBook:NBK10047" ] + "val" : "thoracic part of axial skeleton" }, { "pred" : "hasExactSynonym", - "val" : "neural tube ventricular zone", - "xrefs" : [ "MP:0009689" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "neural tube ependymal zone", - "xrefs" : [ "MP:0009689" ] + "val" : "thoracic skeleton", + "xrefs" : [ "EHDAA2:0002013" ] } ], "xrefs" : [ { - "val" : "EMAPA:17152" - }, { - "val" : "EMAPA:35362" + "val" : "EHDAA2:0002013" }, { - "val" : "EMAPA_RETIRED:16783" + "val" : "FMA:77169" }, { - "val" : "MA:0003193" + "val" : "Wikipedia:Thoracic_skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004061", - "lbl" : "neural tube mantle layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", + "lbl" : "primordial vasculature", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.", - "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "A portion of tissue that will develop into vasculature.", + "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural tube intermediate zone", - "xrefs" : [ "MP:0009690", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "future brain marginal layer", - "xrefs" : [ "EMAPA:35360" ] - } ], "xrefs" : [ { - "val" : "EMAPA:17148" + "val" : "EFO:0003708" }, { - "val" : "EMAPA:35360" + "val" : "TAO:0005076" }, { - "val" : "neuronames:1367" + "val" : "ZFA:0005076" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28109,27 +29804,18 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004062", - "lbl" : "neural tube marginal layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015203", + "lbl" : "non-connected functional system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter.", - "xrefs" : [ "MP:0009691", "http://www.ncbi.nlm.nih.gov/books/NBK10047" ] + "val" : "An anatomical group whose component structures share a common function.", + "xrefs" : [ "AEO:0000093", "AEO:JB", "FBC:DOS", "FBbt:00007278" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural tube marginal zone", - "xrefs" : [ "MP:0009691" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "brain marginal zone" - } ], "xrefs" : [ { - "val" : "EMAPA:17151" + "val" : "AEO:0000093" }, { - "val" : "neuronames:1368" + "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28137,122 +29823,88 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004088", - "lbl" : "orbital region", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", + "lbl" : "lateral structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present.", + "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "content of orbital part of eye", - "xrefs" : [ "FMA:260119" ] - }, { - "pred" : "hasExactSynonym", - "val" : "eye region", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "orbital part of face", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular and peri-ocular region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "orbital content", - "xrefs" : [ "FMA:260119" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "orbital part of eye", - "xrefs" : [ "FMA:72951" ] - } ], - "xrefs" : [ { - "val" : "FMA:260119" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004111", - "lbl" : "anatomical conduit", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", + "lbl" : "circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any tube, opening or passage that connects two distinct anatomical spaces.", + "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "foramen", - "xrefs" : [ "EHDAA2:0003080" ] + "pred" : "hasBroadSynonym", + "val" : "heart" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasNarrowSynonym", - "val" : "foramina", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "pred" : "hasExactSynonym", + "val" : "cardiac pump" }, { - "pred" : "hasRelatedSynonym", - "val" : "opening" + "pred" : "hasExactSynonym", + "val" : "heart or heart like organ" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "ostia" + "pred" : "hasNarrowSynonym", + "val" : "circulatory vessel" }, { "pred" : "hasRelatedSynonym", - "val" : "ostium" - } ], - "xrefs" : [ { - "val" : "AEO:0000080" - }, { - "val" : "EHDAA2:0003080" - }, { - "val" : "FMA:242873" - }, { - "val" : "SCTID:346902003" - }, { - "val" : "Wikipedia:Foramen" + "val" : "cardiac structure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", + "lbl" : "heart plus pericardium", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "heart/pericardium", + "xrefs" : [ "MA:0002449" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37597" }, { + "val" : "MA:0002449" + } ], + "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004120", - "lbl" : "mesoderm-derived structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015808", + "lbl" : "eye epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure that develops (entirely or partially) from the mesoderm.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "An epithelium that is part of a camera-type eye.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesodermal derivative", - "xrefs" : [ "FBbt:00025998" ] + "xrefs" : [ { + "val" : "EMAPA:35957" + }, { + "val" : "MA:0003162" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28260,161 +29912,108 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004121", - "lbl" : "ectoderm-derived structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", + "lbl" : "future central nervous system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure that develops (entirely or partially) from the ectoderm.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "Primordium that develops into the central nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "ectodermal deriviative", - "xrefs" : [ "FBbt:00025990" ] + "val" : "future CNS" + }, { + "pred" : "hasExactSynonym", + "val" : "presumptive central nervous system" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000469" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004128", - "lbl" : "optic vesicle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", + "lbl" : "future nervous system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].", - "xrefs" : [ "GO:0003404", "Wikipedia:Optic_vesicles" ] + "val" : "Primordium that develops into the nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 \"Developmental Biology\"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "evagination" - }, { - "pred" : "hasRelatedSynonym", - "val" : "eye vesicle", - "xrefs" : [ "XAO:0000228" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ocular vesicle", - "xrefs" : [ "VHOG:0000165" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "optic vesicles", - "xrefs" : [ "ZFA:0000050" ] + "pred" : "hasExactSynonym", + "val" : "presumptive nervous system", + "xrefs" : [ "AAO:0000477" ] } ], "xrefs" : [ { - "val" : "AAO:0011039" - }, { - "val" : "EHDAA2:0001320" - }, { - "val" : "EMAPA:16540" - }, { - "val" : "FMA:293357" - }, { - "val" : "NCIT:C34236" - }, { - "val" : "SCTID:362864008" - }, { - "val" : "TAO:0000050" - }, { - "val" : "UMLS:C0231106" - }, { - "val" : "VHOG:0000165" - }, { - "val" : "Wikipedia:Optic_vesicles" - }, { - "val" : "XAO:0000228" - }, { - "val" : "ZFA:0000050" + "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000477" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", - "lbl" : "cardiogenic plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016887", + "lbl" : "entire extraembryonic component", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The first recognizable structure derived from the heart field.", - "xrefs" : [ "GO:0003142" ] + "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", + "xrefs" : [ "AEO:0000195", "AEO:JB" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "myocardial plate", - "xrefs" : [ "EHDAA2:0000215" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac crescent", - "xrefs" : [ "EMAPA:16106" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiogenic crescent", - "xrefs" : [ "GO:0003142" ] + "val" : "extra-embryonic component" }, { - "pred" : "hasRelatedSynonym", - "val" : "heart rudiment" + "pred" : "hasExactSynonym", + "val" : "extraembryonic component", + "xrefs" : [ "AEO:0000195" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0000215" + "val" : "AEO:0000195" }, { - "val" : "EMAPA:16106" + "val" : "EHDAA2:0000003" }, { - "val" : "VHOG:0000975" + "val" : "EMAPA:16042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", - "lbl" : "primary heart field", + "id" : "http://purl.obolibrary.org/obo/UBERON_0019207", + "lbl" : "chorioretinal region", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", - "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] + "val" : "The part of the eye that consists of both the retina and the optic choroid.", + "xrefs" : [ "UBERON:drseb", "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "first heart field", - "xrefs" : [ "XAO:0004185" ] + "val" : "chorioretina" }, { "pred" : "hasExactSynonym", - "val" : "primary heart field", - "xrefs" : [ "PMID:17276708", "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "FHF", - "xrefs" : [ "XAO:0004185" ] + "val" : "choroid and retina" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "PHF", - "xrefs" : [ "XAO:0004185" ] + "pred" : "hasExactSynonym", + "val" : "retinachoroid" }, { - "pred" : "hasRelatedSynonym", - "val" : "heart field", - "xrefs" : [ "XAO:0004185" ] + "pred" : "hasExactSynonym", + "val" : "retinachoroidal region" } ], "xrefs" : [ { - "val" : "XAO:0004185" + "val" : "SCTID:110701000" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28422,42 +30021,37 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", - "lbl" : "heart tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0019261", + "lbl" : "white matter of forebrain", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelial tube that will give rise to the mature heart.", - "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] + "val" : "A white matter that is part of the forebrain.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic heart tube", - "xrefs" : [ "GO:0003143" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial heart tube", - "xrefs" : [ "MP:0012700" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial tube", - "xrefs" : [ "XAO:0000337" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { - "val" : "AAO:0010411" - }, { - "val" : "EFO:0003526" - }, { - "val" : "EMAPA:32685" - }, { - "val" : "NCIT:C34161" + "val" : "DHBA:10557" }, { - "val" : "TAO:0000360" + "val" : "FMA:268634" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "XAO:0000337" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0019304", + "lbl" : "sensory organ epithelium", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EMAPA:35952" }, { - "val" : "ZFA:0000360" + "val" : "MA:0003174" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28465,26 +30059,17 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", - "lbl" : "cardiac chamber", + "id" : "http://purl.obolibrary.org/obo/UBERON_0022288", + "lbl" : "surface of eyeball", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", - "xrefs" : [ "GO:0003205" ] - }, - "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chamber of heart" - }, { - "pred" : "hasExactSynonym", - "val" : "heart chamber" + "pred" : "hasRelatedSynonym", + "val" : "surface of region of wall of eyeball", + "xrefs" : [ "FMA:58315" ] } ], "xrefs" : [ { - "val" : "FMA:7095" - }, { - "val" : "SCTID:276456008" + "val" : "FMA:58315" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28492,108 +30077,82 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004277", - "lbl" : "eye muscle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0022303", + "lbl" : "nervous system cell part layer", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A muscle that is part of the eye region.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].", + "xrefs" : [ "NLX:149357" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "AAO:0000156" - }, { - "val" : "EMAPA:35335" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "lamina", + "xrefs" : [ "CUMBO:CUMBO" ] }, { - "val" : "MA:0000271" + "pred" : "hasBroadSynonym", + "val" : "layer", + "xrefs" : [ "CUMBO:CUMBO" ] + } ], + "xrefs" : [ { + "val" : "NLX:149357" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034705", + "lbl" : "developing neuroepithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "An embryonic or larval epithelium that is committed to form part of the nervous system.", + "xrefs" : [ "AEO:0001008", "AEO:JB" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "neurepithelium", + "xrefs" : [ "BTO:0000314" ] + }, { "pred" : "hasExactSynonym", - "val" : "set of all bones" + "val" : "embryonic neuroepithelium", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "set of bones of body" + "val" : "neuroepithelium", + "xrefs" : [ "AEO:0001008" ] } ], "xrefs" : [ { - "val" : "AEO:0000168" - }, { - "val" : "EHDAA2:0001843" - }, { - "val" : "EHDAA:5047" - }, { - "val" : "EMAPA:17213" - }, { - "val" : "FMA:23875" - }, { - "val" : "GAID:177" - }, { - "val" : "MA:0003006" - }, { - "val" : "MAT:0000032" - }, { - "val" : "MESH:D012863" - }, { - "val" : "MIAA:0000032" - }, { - "val" : "SCTID:361378004" - }, { - "val" : "VSAO:0000026" + "val" : "AEO:0001008" }, { - "val" : "Wikipedia:Skeleton" + "val" : "BTO:0000314" }, { - "val" : "XAO:0004053" + "val" : "EHDAA2_RETIRED:0004654" }, { - "val" : "galen:Skeleton" + "val" : "FMA:64807" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004291", - "lbl" : "heart rudiment", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034706", + "lbl" : "proliferating neuroepithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.", - "xrefs" : [ "GO:0003313" ] + "val" : "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.", + "xrefs" : [ "AEO:0001009" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart cone", - "xrefs" : [ "GO:0003313" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rudimentary heart", - "xrefs" : [ "ZFA:0000115" ] - } ], "xrefs" : [ { - "val" : "TAO:0000115" - }, { - "val" : "ZFA:0000115" + "val" : "AEO:0001009" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28601,23 +30160,16 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004348", - "lbl" : "optic eminence", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034707", + "lbl" : "differentiating neuroepithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The embryonic structure that gives rise to the corneal ectoderm.", - "xrefs" : [ "MP:0006305" ] + "val" : "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.", + "xrefs" : [ "AEO:0001010" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "xrefs" : [ { - "val" : "EHDAA:938" - }, { - "val" : "EMAPA:16322" - }, { - "val" : "RETIRED_EHDAA2:0001308" - }, { - "val" : "VHOG:0001296" + "val" : "AEO:0001010" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28625,4386 +30177,3545 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004367", - "lbl" : "Descemet's membrane", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034713", + "lbl" : "cranial neuron projection bundle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].", - "xrefs" : [ "MP:0004285", "https://github.com/obophenotype/uberon/issues/15" ] + "val" : "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.", + "xrefs" : [ "ISBN:0471888893", "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "Descemet membrane" - }, { - "pred" : "hasExactSynonym", - "val" : "Descemet's posterior elastic lamina", - "xrefs" : [ "FMA:58309" ] - }, { - "pred" : "hasExactSynonym", - "val" : "lamina limitans posterior", - "xrefs" : [ "FMA:58309" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "lamina limitans posterior corneae", - "xrefs" : [ "FMA:58309", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior limiting lamina", - "xrefs" : [ "MA:0001246" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior limiting lamina of cornea", - "xrefs" : [ "FMA:58309" ] - }, { - "pred" : "hasExactSynonym", - "val" : "posterior limiting membrane", - "xrefs" : [ "ZFA:0001686" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:18804" - }, { - "val" : "FMA:58309" - }, { - "val" : "GAID:894" - }, { - "val" : "MA:0001246" - }, { - "val" : "MESH:D003886" - }, { - "val" : "NCIT:C32454" - }, { - "val" : "SCTID:281076002" - }, { - "val" : "TAO:0002157" + "pred" : "hasRelatedSynonym", + "val" : "cranial nerve fiber bundle", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "UMLS:C0011665" + "pred" : "hasRelatedSynonym", + "val" : "cranial nerve fiber tract", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "Wikipedia:Descemet%27s_membrane" + "pred" : "hasRelatedSynonym", + "val" : "cranial nerve or tract", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "ZFA:0001686" + "pred" : "hasRelatedSynonym", + "val" : "neuron projection bundle from brain", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/15" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004370", - "lbl" : "anterior limiting lamina of cornea", + "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", + "lbl" : "multi organ part structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; 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A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "val" : "EHDAA2:0003235" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "EMAPA:36040" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "NCIT:C34131" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "UMLS:C1516779" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "val" : "Wikipedia:Conceptus" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004732", - "lbl" : "segmental subdivision of nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.", - "xrefs" : [ "FBbt:00005140", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neuromere", - "xrefs" : [ "FBbt:00005140" ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004733", - "lbl" : "segmental subdivision of hindbrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ subunit that is part of a hindbrain [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hindbrain segment", - "xrefs" : [ "FMA:61998" ] - }, { - "pred" : "hasExactSynonym", - "val" : "segment of hindbrain", - "xrefs" : [ "FMA:61998" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "FMA:61998" + "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", - "lbl" : "gastrula", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the gastrula stage.", - "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gastrula embryo", - "xrefs" : [ "BILA:0000060" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocystis trilaminaris", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastocyst", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar germ", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } ], + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BILA:0000060" - }, { - "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" - }, { - "val" : "FMA:293108" - }, { - "val" : "GAID:1302" - }, { - "val" : "MESH:D005775" - }, { - "val" : "MIAA:0000179" - }, { - "val" : "NCIT:C34057" - }, { - "val" : "NCIT:C34058" - }, { - "val" : "UMLS:C0017199" - }, { - "val" : "UMLS:C1284022" - }, { - "val" : "Wikipedia:Gastrula" - }, { - "val" : "Wikipedia:Trilaminar_blastocyst" + "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", - "lbl" : "skeletal element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" - }, { - "val" : "galen:SkeletalStructure" + "val" : "GOREL:0002003" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" - }, { - "val" : "MA:0003007" - }, { - "val" : "SCTID:361827000" - }, { - "val" : "VSAO:0000181" + "val" : "GOREL:0002004" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", - "lbl" : "cardiovascular system endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that is part of the cardiovascular system.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "endothelia", - "xrefs" : [ "ZFA:0001639" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "vascular endothelia", - "xrefs" : [ "XAO:0000356" ] - } ], "xrefs" : [ { - "val" : "BTO:0001853" - }, { - "val" : "EMAPA:35201" - }, { - "val" : "GAID:519" - }, { - "val" : "MA:0000717" - }, { - "val" : "MESH:D004730" - }, { - "val" : "NCIT:C13053" - }, { - "val" : "TAO:0002171" - }, { - "val" : "UMLS:C0014261" - }, { - "val" : "VHOG:0001217" - }, { - "val" : "XAO:0000356" - }, { - "val" : "ZFA:0001639" + "val" : "RO:0000053" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'endothelium'" + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004872", - "lbl" : "splanchnic layer of lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" ] + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "visceral mesoderm", - "xrefs" : [ "BILA:0000044", "http://www.drugs.com/dict/visceral-mesoderm.html", "http://www.stedmans.com/" ] - }, { - "pred" : "hasExactSynonym", - "val" : "inner layer of lateral plate mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - } ], "xrefs" : [ { - "val" : "AAO:0011102" - }, { - "val" : "BILA:0000044" - }, { - "val" : "FMA:295568" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" - }, { - "val" : "XAO:0000276" + "val" : "RO:0000056" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], "xrefs" : [ { - "val" : "AAO:0000478" - }, { - "val" : "EFO:0003426" - }, { - "val" : "TAO:0000091" - }, { - "val" : "ZFA:0000091" + "val" : "RO:0000057" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004905", - "lbl" : "articulation", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A proximal-distal subdivision of the digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system subdivision", - "xrefs" : [ "FMA:71131" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut section", - "xrefs" : [ "FBbt:00100315" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "segment of intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "subdivision of alimentary system", - "xrefs" : [ "FMA:71131" ] - } ], - "xrefs" : [ { - "val" : "FBbt:00100315" - }, { - "val" : "FMA:71131" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "lbl" : "organ component layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A part of a wall of an organ that forms a layer.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FMA:82485" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005061", - "lbl" : "neural groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.", - "xrefs" : [ "GO:0001842", "Wikipedia:Neural_groove", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "xrefs" : [ { - "val" : "AAO:0011071" - }, { - "val" : "EMAPA:35594" - }, { - "val" : "FMA:295624" - }, { - "val" : "NCIT:C34224" - }, { - "val" : "SCTID:361463007" - }, { - "val" : "UMLS:C0814992" - }, { - "val" : "Wikipedia:Neural_groove" - }, { - "val" : "XAO:0000248" - }, { - "val" : "neuronames:1363" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "lbl" : "neural fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "One of the two elevated edges of the neural groove[GO,MP].", - "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "medullary fold", - "xrefs" : [ "MP:0011256" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001249" - }, { - "val" : "FMA:295618" - }, { - "val" : "NCIT:C34223" - }, { - "val" : "SCTID:361461009" - }, { - "val" : "UMLS:C0814993" - }, { - "val" : "Wikipedia:Neural_fold" - }, { - "val" : "XAO:0004087" - }, { - "val" : "neuronames:1364" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005068", - "lbl" : "neural rod", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].", - "xrefs" : [ "GO:0014024", "ZFA:0000133" ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural tube rod", - "xrefs" : [ "GO:0014027" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003498" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "val" : "TAO:0000133" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "ZFA:0000133" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005085", - "lbl" : "ectodermal placode", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO].", - "xrefs" : [ "GO:0060788" ] + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "epithelial placode", - "xrefs" : [ "AEO:0000112" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000218" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "lbl" : "muscle structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", - "xrefs" : [ "GO:0061061" ] + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "musculus", - "xrefs" : [ "FMA:30316" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle element" - } ], - "xrefs" : [ { - "val" : "FMA:30316" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", - "lbl" : "epithelial fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelial sheet bent on a linear axis.", - "xrefs" : [ "GO:0060571" ] + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0002007" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005162", - "lbl" : "multi cell part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.", - "xrefs" : [ "CARO:0001000" ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multi-cell-component structure", - "xrefs" : [ "CARO:0001000" ] - }, { - "pred" : "hasExactSynonym", - "val" : "multi-cell-part structure", - "xrefs" : [ "CARO:0001000" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cell part cluster", - "xrefs" : [ "FMA:83115" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011000" - }, { - "val" : "CARO:0001000" - }, { - "val" : "FBbt:00007060" - }, { - "val" : "FMA:83115" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005174", - "lbl" : "dorsal region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "back organ", - "xrefs" : [ "MA:0001901" ] - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal region organ" - } ], + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "xrefs" : [ { - "val" : "EMAPA:37274" - }, { - "val" : "MA:0001901" + "val" : "RO:0002087" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", - "lbl" : "trunk region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An organ or element that part of the trunk region. 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Examples: lung, heart, longus colli.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracic cavity organ", - "xrefs" : [ "MA:0000557" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37273" - }, { - "val" : "MA:0000557" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", - "lbl" : "thoracic segment organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that part of the thoracic segment region. 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There are no endoneurium and schwann cells in the central nervous system.", - "xrefs" : [ "Wikipedia:Nervous_system_fiber" ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "comments" : [ "This is the transitive form of the develops from relation" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + }, + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "nerve fibre", - "xrefs" : [ "FMA:5914" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "neurofibra", - "xrefs" : [ "FMA:5914", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neurofibrum", - "xrefs" : [ "FMA:5914" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "nerve fibers", - "xrefs" : [ "BAMS:nfi" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "neurofibra", - "xrefs" : [ "Wikipedia:Nerve_fiber" ] - } ], - "xrefs" : [ { - "val" : "BAMS:nfi" - }, { - "val" : "FMA:5914" - }, { - "val" : "MESH:D009412" - }, { - "val" : "SCTID:88545005" - }, { - "val" : "Wikipedia:Nervous_system_fiber" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "has developmental precursor" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006135", - "lbl" : "myelinated nerve fiber", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH).", - "xrefs" : [ "ncithesaurus:Myelinated_Nerve_Fiber" ] + "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "FMA:5915" - }, { - "val" : "GAID:745" - }, { - "val" : "MESH:D009413" - }, { - "val" : "NCIT:C12627" - }, { - "val" : "SCTID:362296008" - }, { - "val" : "UMLS:C0027750" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding link to UBERON:0002316 ! white matter of neuraxis" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117569" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006222", - "lbl" : "future diencephalon", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The foremost region of the future forebrain that develops into the diencephalon.", - "xrefs" : [ "UBERON:cjm", "Wikipedia:Diencephalon" ] + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive diencephalon", - "xrefs" : [ "TAO:0000574" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EFO:0003442" - }, { - "val" : "EHDAA2:0000600" - }, { - "val" : "EHDAA:844" - }, { - "val" : "EMAPA:16514" - }, { - "val" : "RETIRED_EHDAA2:0000386" - }, { - "val" : "TAO:0000574" - }, { - "val" : "ZFA:0000574" + "val" : "RO:0002211" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006238", - "lbl" : "future brain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The embryonic precursor of the brain.", - "xrefs" : [ "NLX:94995" ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "brain rudiment", - "xrefs" : [ "TAO:0000146" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive brain", - "xrefs" : [ "ZFA:0000146" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "encephalon", - "xrefs" : [ "NLX:94995" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic brain", - "xrefs" : [ "BTO:0004726" ] - } ], - "xrefs" : [ { - "val" : "BAMS:Enc" - }, { - "val" : "BTO:0004726" - }, { - "val" : "EFO:0003431" - }, { - "val" : "EHDAA:300" - }, { - "val" : "EHDAA:830" - }, { - "val" : "EMAPA:16089" - }, { - "val" : "FMA:312967" - }, { - "val" : "RETIRED_EHDAA2:0000591" - }, { - "val" : "TAO:0000146" - }, { - "val" : "ZFA:0000146" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006240", - "lbl" : "future forebrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A presumptive structure that has the potential to develop into a forebrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future prosencephalon" - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive forebrain", - "xrefs" : [ "ZFA:0000062" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive prosencephalon", - "xrefs" : [ "TAO:0000062" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "prosencephalon", - "xrefs" : [ "EHDAA2:0000661" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BAMS:Pros" - }, { - "val" : "EFO:0003423" - }, { - "val" : "EHDAA2:0000661" - }, { - "val" : "EHDAA:2643" - }, { - "val" : "EMAPA:16640" - }, { - "val" : "TAO:0000062" - }, { - "val" : "Wikipedia:Prosencephalon" - }, { - "val" : "ZFA:0000062" + "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006241", - "lbl" : "future spinal cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord", - "xrefs" : [ "ZFA:0000417" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord neural keel", - "xrefs" : [ "TAO:0000417" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord neural plate", - "xrefs" : [ "TAO:0000417" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive spinal cord neural rod", - "xrefs" : [ "TAO:0000417" ] - } ], + "definition" : { + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "EFO:0003438" - }, { - "val" : "EHDAA2:0000674" - }, { - "val" : "EHDAA:898" - }, { - "val" : "EMAPA:16092" - }, { - "val" : "EMAPA:16755" - }, { - "val" : "TAO:0000417" - }, { - "val" : "ZFA:0000417" + "val" : "RO:0002215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", - "lbl" : "notochordal plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", - "xrefs" : [ "VHOG:0001212" ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "xrefs" : [ { - "val" : "EHDAA2:0001278" - }, { - "val" : "EHDAA:264" - }, { - "val" : "EMAPA:16101" - }, { - "val" : "NCIT:C34231" + "val" : "RO:0002216" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "UMLS:C1518429" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" }, { - "val" : "VHOG:0001212" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002220" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check ordering; awaiting confirmation from JB" + "val" : "This relation acts as a join point with BSPO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "lbl" : "notochordal process", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", - "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] + "val" : "inverse of surrounded by" }, - "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive notochord" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002222", + "lbl" : "temporally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002223", + "lbl" : "starts", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of starts with" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002224", + "lbl" : "starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "EHDAA2:0001279" - }, { - "val" : "EHDAA:224" - }, { - "val" : "EMAPA:16102" - }, { - "val" : "FMA:293135" - }, { - "val" : "NCIT:C34232" - }, { - "val" : "UMLS:C1518430" - }, { - "val" : "VHOG:0001213" + "val" : "RO:0002224" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "starts_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006311", - "lbl" : "chamber of eyeball", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002225", + "lbl" : "develops from part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A segment of the eyeball that is filled with refractive media.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002226", + "lbl" : "develops in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x develops_in y if x is located in y whilst x is developing" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002229", + "lbl" : "ends", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of ends with" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "eye chamber", - "xrefs" : [ "MA:0002459" ] - }, { - "pred" : "hasExactSynonym", - "val" : "eyeball chamber", - "xrefs" : [ "FMA:58071" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "chamber of eye", - "xrefs" : [ "BTO:0002085" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002230", + "lbl" : "ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BTO:0002085" - }, { - "val" : "EMAPA:37529" - }, { - "val" : "FMA:58071" - }, { - "val" : "MA:0002459" - }, { - "val" : "NCIT:C32301" - }, { - "val" : "SCTID:280540004" - }, { - "val" : "UMLS:C0459556" + "val" : "RO:0002230" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006312", - "lbl" : "ocular refractive media", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - 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Insertions are usually connections of muscle via tendon to bone." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/property/insertion" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002375", + "lbl" : "in branching relationship with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007619", - "lbl" : "limiting membrane of retina", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "retina lamina", - "xrefs" : [ "MA:0001318", "https://github.com/obophenotype/uberon/issues/52" ] - } ], - "xrefs" : [ { - "val" : "MA:0001318" + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" }, { - "val" : "SCTID:280667001" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007625", - "lbl" : "pigment epithelium of eye", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.", - "xrefs" : [ "MP:0005200" ] + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of upstream of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "eye pigment epithelium", - "xrefs" : [ "MESH:A09.371.670" ] - } ], "xrefs" : [ { - "val" : "GAID:907" - }, { - "val" : "MESH:D010857" + "val" : "RO:0002404" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007651", - "lbl" : "anatomical junction", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical structure that connects two structures.", - "xrefs" : [ "http://code.google.com/p/caro2/issues/detail?id=15" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "junction" - }, { - "pred" : "hasExactSynonym", - "val" : "anatomical junction" - } ], - "xrefs" : [ { - "val" : "FMA:5898" - }, { - "val" : "SCTID:91833003" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007688", - "lbl" : "anlage", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.", - "xrefs" : [ "FBbt:00005426", "http://flybase.org/reports/FBrf0178740.html" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - 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"val" : "An axon tract that is part of a brain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "brain tract", - "xrefs" : [ "FMA:83848" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "landmark tracts", - "xrefs" : [ "DMBA:tracts" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "FMA:83848" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - 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"val" : "consider merging with vasculature" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007811", - "lbl" : "craniocervical region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cephalic area", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cephalic part of animal", - "xrefs" : [ "Wikipedia:Head" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cephalic region", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/379" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "head and neck", - "xrefs" : [ "FMA:280881" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "head or neck" - } ], - "xrefs" : [ { - "val" : "CALOHA:TS-2356" - }, { - "val" : "EV:0100009" - }, { - "val" : "FMA:280881" - }, { - "val" : "MA:0000006" - }, { - "val" : "NCIT:C12418" - }, { - "val" : "SCTID:361355005" - }, { - "val" : "UMLS:C0460004" - }, { - "val" : "WikipediaCategory:Head_and_neck" - }, { - "val" : "galen:HeadAndNeck" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", - "lbl" : "entire embryonic mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Sum total of mesenchyme in the embryo.", - "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, - "xrefs" : [ { - "val" : "EHDAA2:0001113" - }, { - "val" : "EHDAA:177" - }, { - "val" : "EMAPA:16097" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "OWL does not allow defining object properties via a Union" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", - "lbl" : "subdivision of trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "region of trunk", - "xrefs" : [ "FMA:25054" ] - }, { - "pred" : "hasExactSynonym", - "val" : "trunk subdivision", - "xrefs" : [ "FMA:25054" ] - } ], - "xrefs" : [ { - "val" : "FMA:25054" - }, { - "val" : "SCTID:22943007" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009581", - "lbl" : "midbrain mantle layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mantle layer lateral wall midbrain", - "xrefs" : [ "VHOG:0000910" ] - }, { - "pred" : "hasExactSynonym", - "val" : "midbrain lateral wall mantle layer" - }, { - "pred" : "hasRelatedSynonym", - "val" : "mantle layer lateral wall mesencephalon", - "xrefs" : [ "VHOG:0000910" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001172" - }, { - "val" : "EMAPA:16977" - }, { - "val" : "VHOG:0000910" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009615", - "lbl" : "midbrain hindbrain boundary neural plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "MHB neural plate", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "midbrain-hindbrain boundary neural plate", - "xrefs" : [ "ZFA:0007044" ] - } ], - "xrefs" : [ { - "val" : "TAO:0007044" - }, { - "val" : "ZFA:0007044" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - developmental relationships for lines" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009616", - "lbl" : "presumptive midbrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A presumptive structure that has the potential to develop into a midbrain.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive mesencephalon", - "xrefs" : [ "ZFA:0000148" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "early midbrain", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "future midbrain", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "mesencephalon", - "xrefs" : [ "EHDAA2:0000615" ] - } ], - "xrefs" : [ { - "val" : "BAMS:MES" - }, { - "val" : "EFO:0003432" - }, { - "val" : "EHDAA2:0000615" - }, { - "val" : "EMAPA:16140" - }, { - "val" : "TAO:0000148" - }, { - "val" : "Wikipedia:Mesencephalon" - }, { - "val" : "ZFA:0000148" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - unify naming conventions" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "lbl" : "trunk paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "trunk and cervical paraxial mesenchyme", - "xrefs" : [ "EHDAA2:0002094" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trunk paraxial mesenchyme", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002094" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "exists during" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009881", - "lbl" : "anterior lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - 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"synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "face mesenchyme" - }, { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of face" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:35337" - }, { - "val" : "FMA:302884" + "val" : "RO:0002565" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_movement_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009920", - "lbl" : "optic neural crest", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002567", + "lbl" : "biomechanically related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "EHDAA2:0001315" - 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"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "multicellular structure", - "xrefs" : [ "FBbt:00100313" ] - } ], - "xrefs" : [ { - "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0010096", - 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Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." + }, + "comments" : [ "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "RO:0003000" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "produces" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0010371", - "lbl" : "ecto-epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0003001", + "lbl" : "produced by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelium composed of cells that develops from the ectoderm[FMA,modified].", - 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In most vertebrates this is the rib cage and sternum.", - "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "skeleton of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic part of axial skeleton" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic skeleton", - "xrefs" : [ "EHDAA2:0002013" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002013" - }, { - "val" : "FMA:77169" - }, { - "val" : "Wikipedia:Thoracic_skeleton" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", - "lbl" : "primordial vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", + "lbl" : "protects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A portion of tissue that will develop into vasculature.", - "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] - }, - "xrefs" : [ { - "val" : "EFO:0003708" - }, { - "val" : "TAO:0005076" - }, { - "val" : "ZFA:0005076" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015203", - "lbl" : "non-connected functional system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", + "lbl" : "proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical group whose component structures share a common function.", - "xrefs" : [ "AEO:0000093", "AEO:JB", "FBC:DOS", "FBbt:00007278" ] + "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "xrefs" : [ { - "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "lbl" : "lateral structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", + "lbl" : "sexually_homologous_to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", - "lbl" : "circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", + "lbl" : "site_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "heart" - }, { - "pred" : "hasExactSynonym", - "val" : "cardiac pump" - }, { - "pred" : "hasExactSynonym", - "val" : "heart or heart like organ" - }, { - "pred" : "hasNarrowSynonym", - "val" : "circulatory vessel" - }, { "pred" : "hasRelatedSynonym", - "val" : "cardiac structure" + "val" : "capable_of_has_part" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -33240,599 +33866,496 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", - "lbl" : "heart plus pericardium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", + "lbl" : "subdivision of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart/pericardium", - "xrefs" : [ "MA:0002449" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37597" - }, { - "val" : "MA:0002449" - } ], + "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015808", - "lbl" : "eye epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "An epithelium that is part of a camera-type eye.", - "xrefs" : [ "OBOL:automatic" ] - }, - "xrefs" : [ { - "val" : "EMAPA:35957" - }, { - "val" : "MA:0003162" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - 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"type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "The part of the eye that consists of both the retina and the optic choroid.", - "xrefs" : [ "UBERON:drseb", "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chorioretina" - }, { - "pred" : "hasExactSynonym", - "val" : "choroid and retina" - }, { - "pred" : "hasExactSynonym", - "val" : "retinachoroid" - }, { - "pred" : "hasExactSynonym", - "val" : "retinachoroidal region" - } ], - "xrefs" : [ { - "val" : "SCTID:110701000" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0019261", - "lbl" : "white matter of forebrain", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A white matter that is part of the forebrain.", - "xrefs" : [ "OBOL:automatic" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "xrefs" : [ { - "val" : "DHBA:10557" - }, { - "val" : "FMA:268634" - } ], + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0019304", - "lbl" : "sensory organ epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", "meta" : { - "xrefs" : [ { - "val" : "EMAPA:35952" - }, { - "val" : "MA:0003174" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0022288", - "lbl" : "surface of eyeball", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "surface of region of wall of eyeball", - "xrefs" : [ "FMA:58315" ] - } ], - "xrefs" : [ { - "val" : "FMA:58315" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0022303", - "lbl" : "nervous system cell part layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].", - "xrefs" : [ "NLX:149357" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lamina", - "xrefs" : [ "CUMBO:CUMBO" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "layer", - "xrefs" : [ "CUMBO:CUMBO" ] - } ], - "xrefs" : [ { - "val" : "NLX:149357" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. 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At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034705", - "lbl" : "developing neuroepithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An embryonic or larval epithelium that is committed to form part of the nervous system.", - "xrefs" : [ "AEO:0001008", "AEO:JB" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "neurepithelium", - "xrefs" : [ "BTO:0000314" ] - }, { - "pred" : "hasExactSynonym", - "val" : "embryonic neuroepithelium", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "neuroepithelium", - "xrefs" : [ "AEO:0001008" ] - } ], - "xrefs" : [ { - "val" : "AEO:0001008" - }, { - "val" : "BTO:0000314" - }, { - "val" : "EHDAA2_RETIRED:0004654" - }, { - "val" : "FMA:64807" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034706", - "lbl" : "proliferating neuroepithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.", - "xrefs" : [ "AEO:0001009" ] + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, - "xrefs" : [ { - "val" : "AEO:0001009" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034707", - "lbl" : "differentiating neuroepithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.", - "xrefs" : [ "AEO:0001010" ] + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, - "xrefs" : [ { - "val" : "AEO:0001010" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034713", - "lbl" : "cranial neuron projection bundle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain.", - "xrefs" : [ "ISBN:0471888893", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cranial nerve fiber bundle", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cranial nerve fiber tract", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cranial nerve or tract", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neuron projection bundle from brain", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "xrefs" : [ { - "val" : "CARO:0020001" + "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" + "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035639", - "lbl" : "ocular adnexa", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva.", - "xrefs" : [ "HPO:pr", "UBERON:cjm", "http://medical-dictionary.thefreedictionary.com/ocular+adnexa", "https://github.com/obophenotype/uberon/issues/1132" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "adnexa oculi", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory parts of orbital region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory visual structures", - "xrefs" : [ "FMA:76554", "Wikipedia:Accessory_visual_structures" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "accessory visual structures set", - "xrefs" : [ "FMA:76554" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "adnexal parts of orbital region" - }, { - "pred" : "hasRelatedSynonym", - "val" : "appendage of eye", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "appendages of the eye", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "eye adnexa" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of accessory visual structures", - "xrefs" : [ "FMA:76554" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "structurae oculi accessoriae", - "xrefs" : [ "Wikipedia:Accessory_visual_structures" ] - } ], - "xrefs" : [ { - "val" : "FMA:76554" - }, { - "val" : "NCIT:C32574" - }, { - "val" : "SCTID:120612006" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" }, { - "val" : "UMLS:C0229243" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" }, { - "val" : "Wikipedia:Accessory_visual_structures" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "A synonym type for describing abbreviations or initalisms" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], - "xrefs" : [ { - "val" : "FMA:293105" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036146", - "lbl" : "cardiopharyngeal field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.", - "xrefs" : [ "http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1", "https://orcid.org/0000-0003-3308-6245" ] + "val" : "A synonym type for describing pluralization synonyms" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036215", - "lbl" : "anatomical surface region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity that forms the outermost boundary of an anatomical structure.", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/1324" ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "AAO:0010270" - }, { - "val" : "ZFA:0005594" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", - "lbl" : "visceral muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, - "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral muscle" - } ], + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:17:46Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { @@ -33844,6 +34367,7 @@ "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } @@ -33851,49 +34375,15 @@ "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { @@ -33901,291 +34391,391 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", "lbl" : "latin term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", "lbl" : "plural term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "type" : "PROPERTY", - "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." - }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "type" : "PROPERTY", - "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -34201,11 +34791,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -34222,6 +34814,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -34237,11 +34830,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -34257,23 +34852,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -34283,6 +34907,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -34506,16 +35142,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000483" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000076", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "is_a", @@ -34596,8 +35222,8 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000213" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000117", "pred" : "is_a", @@ -34646,10 +35272,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000132", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000115" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000132", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000710" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000132", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36672,10 +37294,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044249" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009059", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_1901576" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -37844,10 +38462,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0070925", "pred" : "http://purl.obolibrary.org/obo/RO_0002588", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0071704", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0071826", "pred" : "is_a", @@ -38164,14 +38778,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140352", "pred" : "http://purl.obolibrary.org/obo/RO_0002339", "obj" : "http://purl.obolibrary.org/obo/GO_0005576" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1903047", "pred" : "is_a", @@ -38568,6 +39174,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070060", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002198" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -38692,6 +39310,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000036194", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "is_a", @@ -46315,6 +46937,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000005", @@ -46405,10 +47031,10 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000071", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000076" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0004638" + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", @@ -49012,6 +49638,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/subsets/eye_upper_slim.obo b/subsets/eye_upper_slim.obo index b4002a747..afc802901 100644 --- a/subsets/eye_upper_slim.obo +++ b/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -131,7 +136,7 @@ name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell @@ -142,21 +147,21 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] id: CL:0000008 name: migratory cranial neural crest cell def: "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." [https://orcid.org/0000-0001-5208-3432, ZFA:0007091] -xref: ZFA:0007091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000333 ! migratory neural crest cell [Term] id: CL:0000030 name: glioblast subset: cellxgene_subset -xref: ZFA:0009010 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell @@ -168,7 +173,7 @@ subset: cellxgene_subset synonym: "neuroblast" EXACT [] xref: BTO:0000930 xref: FMA:70563 -xref: ZFA:0009011 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata @@ -184,7 +189,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -209,7 +214,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -257,7 +262,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -271,7 +276,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -294,7 +299,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -313,7 +318,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -331,7 +336,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -351,10 +356,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -370,7 +375,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -386,13 +391,13 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -401,12 +406,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -417,7 +420,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -426,7 +429,7 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] @@ -437,7 +440,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesotheliocyte" EXACT [] xref: FMA:66773 -xref: ZFA:0009040 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell @@ -451,7 +454,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -471,10 +474,10 @@ def: "Most generally any neuron which is not motor or sensory. Interneurons may subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0003811 -xref: FBbt:00005125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67313 xref: WBbt:0005113 -xref: ZFA:0009051 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009051 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -484,11 +487,11 @@ name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] subset: human_reference_atlas xref: BTO:0001037 -xref: FBbt:00005124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 xref: MESH:D011984 xref: WBbt:0005759 -xref: ZFA:0009053 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009053 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000526 ! afferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception @@ -502,7 +505,7 @@ def: "A type of interneuron that has two neurites, usually an axon and a dendrit subset: BDS_subset subset: cellxgene_subset xref: FMA:67282 -xref: ZFA:0009055 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070006 ! cortical bipolar morphology @@ -519,15 +522,15 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) -xref: ZFA:0009067 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009067 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) @@ -553,9 +556,9 @@ synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: CALOHA:TS-0415 -xref: FBbt:00005144 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 -xref: ZFA:0009073 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 @@ -569,7 +572,7 @@ synonym: "macrogliocyte" EXACT [] xref: BTO:0000771 xref: CALOHA:TS-2027 xref: FMA:54538 -xref: ZFA:0009074 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) @@ -584,7 +587,7 @@ synonym: "astrocytic glia" EXACT [] xref: BTO:0000099 xref: CALOHA:TS-0060 xref: FMA:54537 -xref: ZFA:0009075 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009075 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000126 ! macroglial cell property_value: RO:0002175 NCBITaxon:9606 @@ -597,9 +600,8 @@ subset: eye_upper_slim subset: human_reference_atlas xref: CALOHA:TS-0172 xref: FMA:70614 -xref: ZFA:0009079 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009079 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell -is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0001985 ! corneal endothelium relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell property_value: RO:0002175 NCBITaxon:9606 @@ -609,7 +611,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -633,7 +635,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -645,7 +647,7 @@ def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 -xref: ZFA:0009090 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009090 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -661,7 +663,7 @@ xref: CALOHA:TS-0613 xref: FMA:70545 xref: MESH:D008544 xref: VHOG:0001679 -xref: ZFA:0009091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome @@ -705,14 +707,14 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -728,7 +730,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -754,20 +756,20 @@ def: "A cell specialized to detect and transduce light." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 -xref: FBbt:00004211 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 -xref: ZFA:0009127 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -775,21 +777,21 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -801,7 +803,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -813,7 +815,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -823,7 +825,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -872,7 +874,7 @@ def: "Any photoreceptor cell that is part of some eye." [FBC:Autogenerated] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas -xref: ZFA:0009154 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye @@ -883,7 +885,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000293 name: structural cell def: "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." [TAIR:sr] -xref: ZFA:0005745 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005745 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -904,7 +906,7 @@ is_a: CL:0000000 ! cell id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -915,7 +917,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -925,7 +927,7 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -934,7 +936,7 @@ name: glioblast (sensu Vertebrata) def: "An early neural cell developing from the early ependymal cell of the neural tube." [GOC:tfm, ISBN:0618947256] synonym: "spongioblast" EXACT [] xref: FMA:70564 -xref: ZFA:0009169 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009169 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000030 ! glioblast is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell @@ -943,7 +945,7 @@ is_a: CL:0011026 ! progenitor cell id: CL:0000342 name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] -xref: ZFA:0009170 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata @@ -953,7 +955,7 @@ id: CL:0000347 name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim -xref: ZFA:0009174 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera @@ -965,7 +967,7 @@ id: CL:0000348 name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim -xref: ZFA:0009175 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid @@ -997,7 +999,7 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1006,7 +1008,7 @@ name: CNS interneuron def: "An interneuron that has its cell body in a central nervous system." [doi:10.1016/B978-0-12-817424-1.00001-X] comment: Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system. subset: human_reference_atlas -xref: ZFA:0009191 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009191 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000099 ! interneuron @@ -1017,7 +1019,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1028,7 +1030,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -1041,7 +1043,7 @@ def: "A neuron which conveys sensory information centrally from the periphery." subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 -xref: ZFA:0009238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -1049,7 +1051,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000529 name: pigmented epithelial cell subset: cellxgene_subset -xref: ZFA:0009241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000710 ! neurecto-epithelial cell [Term] @@ -1063,16 +1065,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1082,7 +1084,7 @@ def: "A cell that originates from the neural crest and differentiates into a pig comment: Derived from UBERON:0002342 neural crest. xref: BTO:0003217 xref: FMA:83377 -xref: ZFA:0009249 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -1141,7 +1143,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -1162,7 +1164,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -1275,7 +1277,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -1318,7 +1320,7 @@ synonym: "ACs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "amacrine neuron" EXACT [] xref: BTO:0004044 xref: FMA:67766 -xref: ZFA:0009255 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009255 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -1333,7 +1335,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1355,7 +1357,7 @@ synonym: "cone" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 -xref: ZFA:0009262 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009262 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -1371,7 +1373,7 @@ synonym: "epithelial cell of cornea" EXACT [FMA:70551] xref: BTO:0004298 xref: CALOHA:TS-0173 xref: FMA:70551 -xref: ZFA:0009264 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009264 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell @@ -1389,7 +1391,7 @@ synonym: "rod" RELATED [doi:10.1038/s41598-020-66092-9] xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 -xref: ZFA:0009275 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009275 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0010009 ! camera-type eye photoreceptor cell relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -1405,7 +1407,7 @@ synonym: "Muller cell" EXACT MISSPELLING [doi:10.21769/BioProtoc.4179] synonym: "Muller glia" EXACT [] synonym: "Müller cell" EXACT [] xref: BTO:0003064 -xref: ZFA:0009280 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009280 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000681 ! radial glial cell is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina @@ -1417,9 +1419,9 @@ name: glutamatergic neuron def: "A neuron that is capable of some neurotansmission by glutamate secretion." [] subset: cellxgene_subset subset: human_reference_atlas -xref: FBbt:00100291 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006829 -xref: ZFA:0009290 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009290 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron @@ -1432,7 +1434,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1446,7 +1448,7 @@ def: "A cell present in the developing CNS. Functions as both a precursor cell a comment: Unlike that of mammals, the brain of adult teleost fish exhibits an intense and widespread neurogenic activity as a result of the persistence of\nradial glial cells acting as neural progenitors throughout life. subset: cellxgene_subset synonym: "forebrain radial glial cell" NARROW [] -xref: ZFA:0009292 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009292 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell relationship: RO:0002202 CL:0000710 ! develops from neurecto-epithelial cell @@ -1470,7 +1472,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1490,7 +1492,7 @@ synonym: "RGCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 -xref: ZFA:0009310 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009310 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) relationship: RO:0002100 UBERON:0000966 ! has soma location retina property_value: RO:0002175 NCBITaxon:9606 @@ -1506,7 +1508,7 @@ synonym: "HC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] xref: BTO:0004120 -xref: ZFA:0009315 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000099 ! interneuron relationship: RO:0002100 UBERON:0003902 ! has soma location retinal neural layer property_value: RO:0002175 NCBITaxon:9606 @@ -1521,7 +1523,7 @@ subset: human_reference_atlas synonym: "BC" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] synonym: "BCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "BPs" RELATED OMO:0003004 [GSE137537] -xref: ZFA:0009318 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009318 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000103 ! bipolar neuron is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0008028 ! visual system neuron @@ -1539,7 +1541,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1556,7 +1558,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -1571,7 +1573,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -1617,7 +1619,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -1665,7 +1667,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1685,7 +1687,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1699,7 +1701,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1713,7 +1715,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1721,12 +1723,12 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1735,12 +1737,12 @@ name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1755,7 +1757,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1764,7 +1766,7 @@ name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:31:08Z [Term] @@ -1776,7 +1778,7 @@ xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell relationship: part_of UBERON:0000965 ! lens of camera-type eye -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:38:03Z [Term] @@ -1788,7 +1790,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1803,8 +1805,8 @@ synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T04:09:27Z [Term] @@ -1820,8 +1822,8 @@ synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T04:09:31Z [Term] @@ -1835,7 +1837,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1846,12 +1848,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1861,9 +1863,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1879,8 +1881,8 @@ is_a: CL:0000005 ! neural crest derived fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T01:57:40Z [Term] @@ -1893,7 +1895,7 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:25:32Z [Term] @@ -1910,7 +1912,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1918,9 +1920,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1934,8 +1936,8 @@ is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium relationship: part_of UBERON:0002506 ! iris epithelium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:28:52Z [Term] @@ -1950,8 +1952,8 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T03:28:27Z [Term] @@ -1970,8 +1972,8 @@ intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T03:37:09Z [Term] @@ -1980,7 +1982,7 @@ name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] is_a: CL:0000048 ! multi fate stem cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T02:38:01Z [Term] @@ -1988,7 +1990,7 @@ id: CL:0005000 name: spinal cord interneuron def: "A CNS interneuron located in the spinal cord." [CL:CVS] comment: Is_a interneuron, part_of UBERON:0002240. -xref: ZFA:0000778 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0000778 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000402 {is_inferred="true"} ! CNS interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0002240 ! has soma location spinal cord @@ -1998,11 +2000,11 @@ relationship: RO:0002100 UBERON:0002240 ! has soma location spinal cord id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2022,7 +2024,7 @@ is_a: CL:0000988 ! hematopoietic cell id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -2048,7 +2050,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-09T19:12:36Z [Term] @@ -2098,7 +2100,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011104 @@ -2130,7 +2132,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2141,7 +2143,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2152,7 +2154,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2189,7 +2191,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system relationship: RO:0002100 UBERON:0001017 ! has soma location central nervous system -property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: terms:contributor http://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:43Z [Term] @@ -2200,8 +2202,8 @@ subset: eye_upper_slim synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4033015 @@ -2215,15 +2217,15 @@ is_a: CL:0009004 ! retinal cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-03-02T14:38:32Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-03-02T14:38:32Z" xsd:dateTime [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -3313,7 +3315,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3832,7 +3833,7 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -3847,7 +3848,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -3860,7 +3861,7 @@ relationship: results_in_assembly_of GO:0042995 ! cell projection id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -4338,7 +4339,7 @@ is_a: GO:0008150 ! biological_process id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -4356,7 +4357,7 @@ relationship: part_of CL:0000000 ! cell id: GO:0043005 name: neuron projection namespace: cellular_component -def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, PMID:3077060] subset: goslim_pir synonym: "nerve fiber" RELATED [GOC:dph] synonym: "neurite" NARROW [] @@ -4618,13 +4619,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -5094,7 +5096,7 @@ creation_date: 2013-12-18T14:04:32Z id: GO:0051649 name: establishment of localization in cell namespace: biological_process -def: "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] +def: "Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] synonym: "establishment of intracellular localization" NARROW [] synonym: "establishment of localisation in cell" EXACT [GOC:mah] @@ -5345,20 +5347,6 @@ relationship: results_in_assembly_of GO:0043226 ! organelle created_by: mah creation_date: 2009-09-15T03:00:51Z -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071826 name: protein-RNA complex organization @@ -5786,27 +5774,6 @@ relationship: has_target_start_location GO:0005622 ! intracellular anatomical st created_by: pg creation_date: 2019-05-22T11:20:45Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1903047 name: mitotic cell cycle process @@ -6528,7 +6495,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -6538,7 +6505,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6550,7 +6517,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6561,7 +6528,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -6571,7 +6538,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6581,7 +6548,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6590,7 +6557,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6603,7 +6570,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6614,7 +6581,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6624,7 +6591,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6637,7 +6604,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -6648,7 +6615,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6657,7 +6624,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6667,7 +6634,7 @@ namespace: quality def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z [Term] @@ -6699,7 +6666,7 @@ xref: ILX:0101312 xref: ilxtr:BipolarPhenotype xref: nifext:2 is_a: PATO:0070027 ! bitufted dendrite cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070027 @@ -6708,7 +6675,7 @@ namespace: quality def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. is_a: PATO:0010006 ! cell morphology -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -6750,6 +6717,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -7099,6 +7069,15 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -7129,6 +7108,18 @@ intersection_of: PR:000000001 ! protein intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -7206,7 +7197,7 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7221,7 +7212,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7305,8 +7296,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000047 @@ -7362,7 +7353,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7528,7 +7519,7 @@ is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -7573,7 +7564,7 @@ xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string [Term] @@ -7726,7 +7717,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -7806,7 +7797,7 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005099 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NLX:147821 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection @@ -7859,7 +7850,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -7883,7 +7874,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -7942,7 +7933,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -7965,7 +7956,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -8025,7 +8016,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8060,7 +8051,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8088,7 +8079,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8113,7 +8104,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8150,7 +8141,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -8204,7 +8195,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8248,7 +8239,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8284,7 +8275,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8304,7 +8295,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -8331,7 +8322,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8366,7 +8357,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8399,7 +8390,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8420,7 +8411,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -8449,7 +8440,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000488 @@ -8566,7 +8557,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -8587,7 +8578,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -8607,7 +8598,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8641,7 +8632,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8659,7 +8650,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8679,7 +8670,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8696,8 +8687,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8723,7 +8714,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8740,7 +8731,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -8763,7 +8754,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8776,7 +8767,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -8891,9 +8882,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -8930,7 +8921,7 @@ xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 -xref: FBbt:00005095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:50801 xref: GAID:571 xref: galen:Brain @@ -8959,8 +8950,8 @@ relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous s relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -8978,7 +8969,7 @@ is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: RO:0000086 PATO:0002124 ! has quality laminar -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] @@ -9029,7 +9020,7 @@ intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI [Term] id: UBERON:0000964 @@ -9077,7 +9068,7 @@ relationship: RO:0002202 UBERON:0004348 ! develops from optic eminence relationship: RO:0002202 UBERON:0005427 ! develops from corneal primordium relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -9177,7 +9168,7 @@ relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region relationship: RO:0002202 UBERON:0003072 {source="EHDAA2"} ! develops from optic cup -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6656 property_value: RO:0002175 NCBITaxon:9606 @@ -9199,7 +9190,7 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -9271,7 +9262,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9321,7 +9312,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -9360,7 +9351,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -9386,7 +9377,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9414,8 +9405,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -9446,7 +9437,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9485,7 +9476,7 @@ synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 -xref: FBbt:00005100 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005100 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle @@ -9537,7 +9528,7 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007692 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9552,7 +9543,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001048 @@ -9571,7 +9562,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -9618,7 +9609,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9634,7 +9625,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9695,7 +9686,7 @@ intersection_of: has_part CL:0000192 ! smooth muscle cell relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber relationship: RO:0002473 CL:0000192 ! composed primarily of smooth muscle cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI [Term] id: UBERON:0001136 @@ -9727,7 +9718,7 @@ intersection_of: part_of UBERON:0000042 ! serous membrane intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm relationship: part_of UBERON:0000042 ! serous membrane relationship: RO:0002473 CL:0000077 {source="FMA"} ! composed primarily of mesothelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI [Term] id: UBERON:0001137 @@ -9752,7 +9743,7 @@ xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] id: UBERON:0001434 @@ -9833,7 +9824,7 @@ xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head relationship: has_part UBERON:0000165 ! mouth relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] id: UBERON:0001555 @@ -9857,7 +9848,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -9901,7 +9892,7 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -9964,7 +9955,7 @@ relationship: capable_of GO:0060082 ! eye blink reflex relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye relationship: protects UBERON:0010409 ! ocular surface region relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI [Term] id: UBERON:0001766 @@ -9995,7 +9986,7 @@ xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001768 @@ -10029,7 +10020,7 @@ relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI property_value: IAO:0000116 "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} @@ -10118,7 +10109,7 @@ intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10154,7 +10145,7 @@ relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball relationship: RO:0000086 PATO:0000963 ! has quality opaque relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10193,7 +10184,7 @@ relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10237,7 +10228,7 @@ relationship: overlaps UBERON:0001802 {source="Wikipedia"} ! posterior segment o relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: IAO:0000116 "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -10276,7 +10267,7 @@ relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea relationship: part_of UBERON:0000964 ! cornea relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI [Term] id: UBERON:0001778 @@ -10381,7 +10372,7 @@ relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor la relationship: adjacent_to UBERON:0003902 ! retinal neural layer relationship: has_part GO:0048770 ! pigment granule relationship: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10412,7 +10403,7 @@ is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001788 ! outer limiting layer of retina relationship: has_part CL:0000287 {source="ZFA"} ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001788 @@ -10602,7 +10593,7 @@ relationship: adjacent_to UBERON:0001793 ! nerve fiber layer of retina relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer relationship: RO:0002473 CL:0000740 ! composed primarily of retinal ganglion cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10719,7 +10710,7 @@ relationship: overlaps CL:0000740 ! retinal ganglion cell relationship: overlaps CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001796 @@ -10750,7 +10741,7 @@ is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid relationship: part_of UBERON:0001766 ! anterior chamber of eyeball relationship: RO:0002433 UBERON:0001766 ! contributes to morphology of anterior chamber of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001797 @@ -10785,7 +10776,7 @@ is_a: UBERON:0006312 ! ocular refractive media relationship: part_of UBERON:0001798 ! vitreous body relationship: RO:0000086 PATO:0000964 ! has quality transparent relationship: RO:0001025 UBERON:0005606 ! located in hyaloid cavity -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001798 @@ -10808,7 +10799,7 @@ is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball relationship: RO:0002254 UBERON:0002346 ! has developmental contribution from neurectoderm relationship: RO:0002473 UBERON:0001797 ! composed primarily of vitreous humor -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: IAO:0000116 "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string [Term] @@ -10865,7 +10856,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI [Term] id: UBERON:0001802 @@ -10893,7 +10884,7 @@ is_a: UBERON:0000063 ! organ subunit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001811 @@ -10930,7 +10921,7 @@ relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10976,7 +10967,7 @@ disjoint_from: UBERON:0002298 ! brainstem relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0006240 ! immediate transformation of future forebrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11026,7 +11017,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre relationship: RO:0002254 UBERON:0003849 ! has developmental contribution from mesencephalic neural crest relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0009616 {source="Bgee:AN"} ! immediate transformation of presumptive midbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI property_value: IAO:0000116 "developmental relationships need revised" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11089,7 +11080,7 @@ relationship: part_of UBERON:0001890 ! forebrain relationship: RO:0002254 UBERON:0003851 ! has developmental contribution from diencephalon neural crest relationship: RO:0002433 UBERON:0001890 ! contributes to morphology of forebrain relationship: RO:0002495 UBERON:0006222 ! immediate transformation of future diencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001896 @@ -11144,7 +11135,7 @@ relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11189,9 +11180,9 @@ relationship: part_of UBERON:0002104 ! visual system relationship: part_of UBERON:0003931 ! diencephalic white matter relationship: RO:0002134 UBERON:0000966 ! innervates retina relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11235,7 +11226,7 @@ is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem relationship: RO:0002202 UBERON:0010285 {source="ZFA"} ! develops from midbrain basal plate -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11321,7 +11312,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11357,7 +11348,7 @@ intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball relationship: part_of UBERON:0000964 ! cornea relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11420,7 +11411,7 @@ xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002028 @@ -11466,7 +11457,7 @@ relationship: overlaps UBERON:0002298 ! brainstem relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} property_value: RO:0002175 NCBITaxon:9606 @@ -11488,7 +11479,7 @@ is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11510,7 +11501,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11718,8 +11709,8 @@ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11782,8 +11773,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002240 @@ -11844,9 +11835,9 @@ relationship: part_of UBERON:0001017 ! central nervous system relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11892,7 +11883,7 @@ relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum relationship: RO:0002150 UBERON:0002240 ! continuous with spinal cord relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI [Term] id: UBERON:0002316 @@ -11929,8 +11920,8 @@ xref: Wikipedia:White_matter xref: ZFA:0001682 is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: RO:0002473 UBERON:0006135 ! composed primarily of myelinated nerve fiber -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -11954,7 +11945,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12011,7 +12002,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12052,7 +12043,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -12094,8 +12085,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12118,7 +12109,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12296,7 +12287,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -12507,7 +12498,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003071 @@ -12604,7 +12595,7 @@ intersection_of: RO:0002387 UBERON:0000965 ! has potential to develop into lens relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye relationship: RO:0002256 UBERON:0004128 ! developmentally induced by optic vesicle relationship: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -12639,7 +12630,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003076 @@ -12684,7 +12675,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003080 @@ -12733,7 +12724,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -12783,7 +12774,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003098 @@ -12811,7 +12802,7 @@ is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034705 {source="EHDAA2"} ! developing neuroepithelium relationship: part_of UBERON:0001894 ! diencephalon relationship: RO:0002202 UBERON:0003072 ! develops from optic cup -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003099 @@ -12897,7 +12888,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -13203,7 +13194,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -13402,7 +13393,7 @@ relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye relationship: RO:0002202 UBERON:0002346 {source="GO-def"} ! develops from neurectoderm relationship: RO:0002202 UBERON:0003071 {source="ZFA"} ! develops from eye primordium relationship: RO:0002256 UBERON:0004880 ! developmentally induced by chordamesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI [Term] id: UBERON:0004139 @@ -13697,8 +13688,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13791,7 +13782,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -13915,7 +13906,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -13931,7 +13922,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -14046,7 +14037,7 @@ synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 -xref: FBbt:00007060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83115 is_a: UBERON:0000061 ! anatomical structure relationship: RO:0002473 GO:0005575 ! composed primarily of cellular_component @@ -14181,7 +14172,7 @@ xref: VHOG:0000456 xref: Wikipedia:Myelencephalon is_a: UBERON:0004733 ! segmental subdivision of hindbrain relationship: RO:0002495 UBERON:0010096 ! immediate transformation of future myelencephalon -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0005291 @@ -14204,7 +14195,7 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000970 ! eye @@ -14235,7 +14226,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -14471,7 +14462,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -15217,7 +15208,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15420,7 +15411,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -15592,11 +15583,11 @@ xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010912 @@ -15658,7 +15649,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -15948,7 +15939,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -16185,7 +16176,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -16276,8 +16267,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Typedef] id: BFO:0000067 @@ -17352,8 +17343,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17361,8 +17352,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17371,8 +17362,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -17523,16 +17514,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -17541,6 +17536,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -17558,6 +17554,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -17776,6 +17773,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -18234,18 +18232,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/subsets/eye_upper_slim.owl b/subsets/eye_upper_slim.owl index a35d2da8e..96eb56261 100644 --- a/subsets/eye_upper_slim.owl +++ b/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4516,6 +4522,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4527,6 +4535,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4537,6 +4546,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4549,6 +4559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4567,6 +4578,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4596,6 +4608,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4704,6 +4717,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4715,6 +4729,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4726,6 +4741,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -5685,15 +5701,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - @@ -5710,17 +5725,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -6017,7 +6025,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -6225,7 +6238,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -10003,7 +10015,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -10046,7 +10058,7 @@ radial glial cells acting as neural progenitors throughout life. A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10085,7 +10097,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -10129,7 +10141,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cell derived from mesoderm or mesenchyme. - 2010-06-29T03:49:14Z + 2010-06-29T03:49:14Z FMA:69076 ZFA:0009388 epithelial mesenchymal cell @@ -10157,7 +10169,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -10184,7 +10196,7 @@ radial glial cells acting as neural progenitors throughout life. Epithelial cells derived from general body ectoderm and ectoderm placodes. - 2010-08-26T08:31:08Z + 2010-08-26T08:31:08Z FMA:70556 general ecto-epithelial cell @@ -10210,7 +10222,7 @@ radial glial cells acting as neural progenitors throughout life. A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. - 2010-09-07T10:38:03Z + 2010-09-07T10:38:03Z FMA:70950 vertebrate lens cell @@ -10248,7 +10260,7 @@ radial glial cells acting as neural progenitors throughout life. A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -10274,7 +10286,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. - 2010-09-13T04:09:27Z + 2010-09-13T04:09:27Z FMA:70606 PE cell @@ -10317,7 +10329,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of non-pigmented ciliary epithelium. This cell type participates in aqueous humor formation by releasing solute, principally sodium and chloride ions received from pigmented epithelial cells via gap junctions, into the aqueous humor of the eye. - 2010-09-13T04:09:31Z + 2010-09-13T04:09:31Z FMA:70607 NPE cell nonpigmented ciliary epithelial cell @@ -10378,7 +10390,7 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -10417,7 +10429,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -10447,7 +10459,7 @@ radial glial cells acting as neural progenitors throughout life. A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -10493,7 +10505,7 @@ radial glial cells acting as neural progenitors throughout life. A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. - 2010-09-22T01:57:40Z + 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte @@ -10535,7 +10547,7 @@ radial glial cells acting as neural progenitors throughout life. A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. - 2010-12-03T03:25:32Z + 2010-12-03T03:25:32Z retinal melanocyte @@ -10572,7 +10584,7 @@ radial glial cells acting as neural progenitors throughout life. A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -10596,7 +10608,7 @@ radial glial cells acting as neural progenitors throughout life. An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -10641,7 +10653,7 @@ radial glial cells acting as neural progenitors throughout life. A pigment cell located in the epithelium of the iris. - 2011-03-01T05:28:52Z + 2011-03-01T05:28:52Z iris pigment epithelial cell @@ -10686,7 +10698,7 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. - 2011-03-06T03:28:27Z + 2011-03-06T03:28:27Z @@ -10739,7 +10751,7 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. - 2011-03-06T03:37:09Z + 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 @@ -10768,7 +10780,7 @@ radial glial cells acting as neural progenitors throughout life. A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. - 2011-08-16T02:38:01Z + 2011-08-16T02:38:01Z retinal progenitor cell @@ -10847,7 +10859,7 @@ radial glial cells acting as neural progenitors throughout life. Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -11230,7 +11242,7 @@ plexiform layer. Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -11266,7 +11278,7 @@ plexiform layer. Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -11301,7 +11313,7 @@ plexiform layer. Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -11433,8 +11445,8 @@ plexiform layer. Any neuron that is part of a central nervous system. - - 2014-06-25T01:17:43Z + + 2014-06-25T01:17:43Z CL:2000029 central nervous system neuron @@ -11585,7 +11597,6 @@ plexiform layer. Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 - Reactome:69278 @@ -14135,7 +14146,6 @@ plexiform layer. - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -15475,7 +15485,7 @@ plexiform layer. A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -15527,7 +15537,7 @@ plexiform layer. Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:18391171 @@ -15562,7 +15572,6 @@ plexiform layer. ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -16876,7 +16885,7 @@ plexiform layer. A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -16920,7 +16929,7 @@ plexiform layer. A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:3077060 @@ -17606,6 +17615,7 @@ plexiform layer. The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite primary metabolism biological_process GO:0044238 @@ -17621,7 +17631,6 @@ plexiform layer. The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators - http://www.metacyc.org @@ -18884,7 +18893,7 @@ plexiform layer. - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. + Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell @@ -18897,7 +18906,7 @@ plexiform layer. - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. + Any process, occurring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph @@ -19547,31 +19556,6 @@ plexiform layer. - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism - biological_process - GO:0071704 - - organic substance metabolic process - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - GOC:mah - - - - @@ -20845,63 +20829,6 @@ plexiform layer. - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -23041,6 +22968,14 @@ plexiform layer. + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -23963,6 +23898,39 @@ plexiform layer. + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -24067,6 +24035,58 @@ plexiform layer. + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -25140,7 +25160,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) EHDAA2:0001968 @@ -25163,7 +25183,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -25176,7 +25196,7 @@ plexiform layer. - + EHDAA2 @@ -25525,7 +25545,7 @@ plexiform layer. - + @@ -25561,14 +25581,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -25976,15 +25996,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -26021,34 +26041,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -27133,7 +27153,7 @@ plexiform layer. - + @@ -27175,14 +27195,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27704,7 +27724,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27739,14 +27759,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27786,7 +27806,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27821,14 +27841,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27869,7 +27889,7 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27910,14 +27930,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28105,7 +28125,7 @@ plexiform layer. - + @@ -28167,14 +28187,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -28284,7 +28304,7 @@ plexiform layer. - + @@ -28356,14 +28376,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -28405,7 +28425,7 @@ plexiform layer. - + @@ -28424,7 +28444,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -28483,11 +28503,11 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -28500,13 +28520,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -28756,9 +28776,9 @@ plexiform layer. - - + + @@ -28842,34 +28862,34 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + MA - + MA - + FMA-isa @@ -29046,10 +29066,10 @@ plexiform layer. - - + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -29097,44 +29117,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -29189,8 +29209,8 @@ plexiform layer. - - + + @@ -29222,24 +29242,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29628,7 +29648,7 @@ plexiform layer. - + @@ -29678,14 +29698,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29751,7 +29771,7 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29796,7 +29816,7 @@ plexiform layer. central nervous system - + @@ -29810,7 +29830,7 @@ plexiform layer. - + Bgee:AN @@ -30463,7 +30483,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -30488,14 +30508,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -30791,7 +30811,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30828,14 +30848,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -30890,7 +30910,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -30913,7 +30933,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -30932,7 +30952,7 @@ plexiform layer. - + FMA @@ -31050,7 +31070,7 @@ plexiform layer. - + @@ -31096,14 +31116,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31369,7 +31389,7 @@ plexiform layer. - + @@ -31408,14 +31428,14 @@ plexiform layer. iris - + - + XAO @@ -31469,7 +31489,7 @@ plexiform layer. - + @@ -31518,14 +31538,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31613,15 +31633,15 @@ plexiform layer. - - + + - + @@ -31656,34 +31676,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31725,7 +31745,7 @@ plexiform layer. - + @@ -31763,14 +31783,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31808,14 +31828,14 @@ plexiform layer. - + - + @@ -31876,24 +31896,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32086,9 +32106,9 @@ plexiform layer. - - + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32108,15 +32128,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32129,19 +32149,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32257,7 +32277,7 @@ plexiform layer. - + @@ -32315,14 +32335,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32398,7 +32418,7 @@ plexiform layer. - + @@ -32430,14 +32450,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -32930,7 +32950,7 @@ plexiform layer. - + @@ -32986,7 +33006,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -32999,7 +33019,7 @@ plexiform layer. - + FMA @@ -33053,7 +33073,7 @@ plexiform layer. - + @@ -33108,14 +33128,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33805,7 +33825,7 @@ plexiform layer. - + @@ -33837,14 +33857,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -33888,7 +33908,7 @@ plexiform layer. - + @@ -33918,14 +33938,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -33962,9 +33982,9 @@ plexiform layer. - - + + @@ -34012,15 +34032,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34033,19 +34053,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34203,7 +34223,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34249,14 +34269,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34727,7 +34747,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34766,14 +34786,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -34941,8 +34961,8 @@ plexiform layer. - - + + @@ -34955,7 +34975,7 @@ plexiform layer. - + @@ -35009,34 +35029,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35365,7 +35385,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35408,14 +35428,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -36046,7 +36066,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36068,14 +36088,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -36279,7 +36299,7 @@ plexiform layer. - + @@ -36353,14 +36373,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - + ZFA @@ -36815,9 +36835,9 @@ plexiform layer. - - + + @@ -36865,15 +36885,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -36892,19 +36912,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36944,8 +36964,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -36983,11 +37003,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -37000,13 +37020,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37068,22 +37088,22 @@ plexiform layer. - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37116,45 +37136,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37440,7 +37460,7 @@ plexiform layer. - + @@ -37493,14 +37513,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37540,8 +37560,8 @@ plexiform layer. - - + + @@ -37567,11 +37587,11 @@ plexiform layer. iris epithelium - + - + @@ -37584,13 +37604,13 @@ plexiform layer. - + MA - + MP @@ -37729,7 +37749,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37746,7 +37766,7 @@ plexiform layer. cranial placode - + @@ -37759,7 +37779,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -37959,7 +37979,7 @@ plexiform layer. - + @@ -37972,7 +37992,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38001,24 +38021,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38140,7 +38160,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38163,14 +38183,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38337,7 +38357,7 @@ plexiform layer. - + @@ -38374,7 +38394,7 @@ plexiform layer. eye primordium - + @@ -38387,7 +38407,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38437,8 +38457,8 @@ plexiform layer. - - + + @@ -38466,24 +38486,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38539,7 +38559,7 @@ plexiform layer. - + @@ -38577,7 +38597,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38590,7 +38610,7 @@ plexiform layer. - + ZFA @@ -38629,9 +38649,9 @@ plexiform layer. - - + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38660,34 +38680,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38762,7 +38782,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38788,7 +38808,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38801,7 +38821,7 @@ plexiform layer. - + Bgee:AN @@ -38877,7 +38897,7 @@ plexiform layer. - + @@ -38917,7 +38937,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38930,7 +38950,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -38980,15 +39000,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39005,15 +39025,15 @@ plexiform layer. heart primordium - + - + - + @@ -39026,19 +39046,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39067,8 +39087,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39092,11 +39112,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -39115,13 +39135,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39442,7 +39462,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39454,14 +39474,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40236,7 +40256,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40251,14 +40271,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40351,7 +40371,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40382,14 +40402,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40642,7 +40662,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40659,7 +40679,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40672,7 +40692,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41074,9 +41094,9 @@ plexiform layer. - - + + @@ -41108,34 +41128,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41231,8 +41251,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41244,24 +41264,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41314,7 +41334,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41333,14 +41353,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41417,7 +41437,7 @@ plexiform layer. - + @@ -41433,14 +41453,14 @@ plexiform layer. eye muscle - + - + MA @@ -41623,7 +41643,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41652,14 +41672,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -42409,7 +42429,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42423,14 +42443,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42457,7 +42477,7 @@ plexiform layer. - + @@ -42496,14 +42516,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -43355,7 +43375,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43376,14 +43396,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43441,7 +43461,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43457,14 +43477,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -43979,7 +43999,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -43987,7 +44007,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44006,7 +44026,7 @@ plexiform layer. - + ZFA @@ -44029,7 +44049,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44047,14 +44067,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44244,7 +44264,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44254,7 +44274,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44273,7 +44293,7 @@ plexiform layer. - + AEO-modified-relation @@ -44330,8 +44350,8 @@ plexiform layer. - - + + @@ -44348,11 +44368,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44365,13 +44385,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44613,7 +44633,7 @@ plexiform layer. - + @@ -44636,14 +44656,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44819,7 +44839,7 @@ plexiform layer. - + @@ -44843,14 +44863,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -44887,7 +44907,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44901,7 +44921,7 @@ plexiform layer. notochordal plate - + @@ -44914,7 +44934,7 @@ plexiform layer. - + EHDAA2 @@ -44942,7 +44962,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44959,14 +44979,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -46007,8 +46027,8 @@ plexiform layer. - - + + @@ -46034,24 +46054,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46102,7 +46122,7 @@ plexiform layer. - + @@ -46121,14 +46141,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46274,7 +46294,7 @@ plexiform layer. - + @@ -46300,7 +46320,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46316,7 +46336,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46398,7 +46418,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46406,7 +46426,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46419,7 +46439,7 @@ plexiform layer. - + Obol @@ -46494,7 +46514,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46502,7 +46522,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46515,7 +46535,7 @@ plexiform layer. - + AEO @@ -46754,7 +46774,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46764,14 +46784,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46799,7 +46819,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46816,14 +46836,14 @@ plexiform layer. vascular system - + - + MA @@ -46944,7 +46964,7 @@ plexiform layer. - + @@ -46961,14 +46981,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47064,7 +47084,7 @@ plexiform layer. - + @@ -47080,14 +47100,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47120,14 +47140,14 @@ plexiform layer. - + - + @@ -47152,24 +47172,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47215,7 +47235,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47223,14 +47243,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47253,7 +47273,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47263,14 +47283,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47326,14 +47346,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47346,7 +47366,7 @@ plexiform layer. - + EHDAA2 @@ -47487,7 +47507,7 @@ plexiform layer. - + @@ -47510,14 +47530,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47558,8 +47578,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47573,11 +47593,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47590,13 +47610,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47625,7 +47645,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47634,14 +47654,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -47944,8 +47964,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -47957,11 +47977,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -47974,13 +47994,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48041,7 +48061,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48051,7 +48071,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48064,7 +48084,7 @@ plexiform layer. - + cjm @@ -48186,7 +48206,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48196,14 +48216,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48465,7 +48485,7 @@ plexiform layer. - + @@ -48507,7 +48527,7 @@ plexiform layer. anterior uvea - + @@ -48520,7 +48540,7 @@ plexiform layer. - + MP @@ -49313,7 +49333,7 @@ plexiform layer. - + @@ -49336,7 +49356,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49349,7 +49369,7 @@ plexiform layer. - + AEO @@ -50339,5 +50359,5 @@ plexiform layer. - + diff --git a/subsets/eye_upper_slim.tsv b/subsets/eye_upper_slim.tsv index 1d366ed5e..f6a93c692 100644 --- a/subsets/eye_upper_slim.tsv +++ b/subsets/eye_upper_slim.tsv @@ -1,315 +1,315 @@ ?x ?label -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1001 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1016 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1022 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1031 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1037 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1043 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1051 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1058 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1065 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1074 -_:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid1088 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+_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid760 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid779 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid795 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid802 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid813 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid819 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid836 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid842 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid851 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid861 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid909 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid959 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid969 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid976 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid983 +_:B5cf462a4X2Deb9eX2D4a6bX2Db4a9X2Dfafc9010b27bgenid990 "cell" "neural crest derived fibroblast" "neuronal receptor cell" @@ -682,7 +682,6 @@ _:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid990 "extracellular exosome" "anchoring junction" "organelle assembly" - "organic substance metabolic process" "protein-RNA complex organization" "cellular component organization or biogenesis" "cell periphery" @@ -717,7 +716,6 @@ _:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid990 "mitotic nuclear division" "extracellular vesicle biogenesis" "export from cell" - "organic substance biosynthetic process" "mitotic cell cycle process" "regulation of blood circulation" "extracellular vesicle" @@ -840,9 +838,11 @@ _:B8a48f5f4X2D2068X2D44f9X2Daa24X2D5b1a69e75fddgenid990 "lymphocyte antigen 76 (mouse)" "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "eukaryotic protein" + "protein-containing molecular entity" "processual entity" "camera-type eye" "sense organ" diff --git a/subsets/general_cell_types_upper_slim.json b/subsets/general_cell_types_upper_slim.json index effd7a8d6..a7dcbb071 100644 --- a/subsets/general_cell_types_upper_slim.json +++ b/subsets/general_cell_types_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -3182,62 +3029,6 @@ "val" : "CALOHA:TS-2109" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000323", "lbl" : "lytic vacuole", @@ -3405,6 +3196,24 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0001677", + "lbl" : "formation of translation initiation ternary complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", + "xrefs" : [ "GOC:hjd" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "translation initiation ternary complex assembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0001704", "lbl" : "formation of primary germ layer", @@ -4583,6 +4392,144 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006412", + "lbl" : "translation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein anabolism" + }, { + "pred" : "hasExactSynonym", + "val" : "protein biosynthesis" + }, { + "pred" : "hasExactSynonym", + "val" : "protein biosynthetic process" + }, { + "pred" : "hasExactSynonym", + "val" : "protein formation" + }, { + "pred" : "hasExactSynonym", + "val" : "protein synthesis" + }, { + "pred" : "hasExactSynonym", + "val" : "protein translation" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Translation_(genetics)" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006416" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006453" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043037" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006413", + "lbl" : "translational initiation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.", + "xrefs" : [ "ISBN:019879276X" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "biopolymerisation" + }, { + "pred" : "hasBroadSynonym", + "val" : "biopolymerization" + }, { + "pred" : "hasBroadSynonym", + "val" : "protein synthesis initiation" + }, { + "pred" : "hasExactSynonym", + "val" : "translation initiation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006440" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006454" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006414", + "lbl" : "translational elongation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.", + "xrefs" : [ "GOC:ems" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "protein synthesis elongation" + }, { + "pred" : "hasExactSynonym", + "val" : "translation elongation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006442" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006455" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006415", + "lbl" : "translational termination", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).", + "xrefs" : [ "GOC:hjd", "ISBN:019879276X" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "protein synthesis termination" + }, { + "pred" : "hasExactSynonym", + "val" : "translation termination" + }, { + "pred" : "hasExactSynonym", + "val" : "translational complex disassembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006443" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006456" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006810", "lbl" : "transport", @@ -4646,7 +4593,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", + "val" : "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.", "xrefs" : [ "GOC:mah", "ISBN:0716731363", "PMID:22323285" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -6074,6 +6021,59 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0019538", + "lbl" : "protein metabolic process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways involving a protein. Includes protein modification.", + "xrefs" : [ "GOC:ma" ] + }, + "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular protein metabolic process" + }, { + "pred" : "hasExactSynonym", + "val" : "cellular protein metabolism" + }, { + "pred" : "hasExactSynonym", + "val" : "protein metabolic process and modification" + }, { + "pred" : "hasExactSynonym", + "val" : "protein metabolism" + }, { + "pred" : "hasExactSynonym", + "val" : "protein metabolism and modification" + }, { + "pred" : "hasNarrowSynonym", + "val" : "multicellular organismal protein metabolic process" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Protein_metabolism" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/23112" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27189" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006411" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044267" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0044268" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0019724", "lbl" : "B cell mediated immunity", @@ -6148,6 +6148,35 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022411", + "lbl" : "cellular component disassembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process that results in the breakdown of a cellular component.", + "xrefs" : [ "GOC:isa_complete" ] + }, + "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cell structure disassembly" + }, { + "pred" : "hasExactSynonym", + "val" : "cellular component disassembly at cellular level" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27189" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071845" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0022414", "lbl" : "reproductive process", @@ -6197,6 +6226,79 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022607", + "lbl" : "cellular component assembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The aggregation, arrangement and bonding together of a cellular component.", + "xrefs" : [ "GOC:isa_complete" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cell structure assembly" + }, { + "pred" : "hasExactSynonym", + "val" : "cellular component assembly at cellular level" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071844" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022613", + "lbl" : "ribonucleoprotein complex biogenesis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.", + "xrefs" : [ "GOC:isa_complete", "GOC:mah" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "RNA-protein complex biogenesis", + "xrefs" : [ "GOC:mah" ] + }, { + "pred" : "hasExactSynonym", + "val" : "ribonucleoprotein complex biogenesis and assembly", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0022618", + "lbl" : "protein-RNA complex assembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.", + "xrefs" : [ "GOC:jl" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "RNA-protein complex assembly" + }, { + "pred" : "hasExactSynonym", + "val" : "RNP complex assembly" + }, { + "pred" : "hasExactSynonym", + "val" : "ribonucleoprotein complex assembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0023052", "lbl" : "signaling", @@ -6305,7 +6407,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -6335,7 +6437,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -6966,6 +7068,45 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0032984", + "lbl" : "protein-containing complex disassembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The disaggregation of a protein-containing macromolecular complex into its constituent components.", + "xrefs" : [ "GOC:mah" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein complex disassembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecule complex disassembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular protein complex disassembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecule complex disassembly" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22580" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034623" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043241" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043624" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032991", "lbl" : "protein-containing complex", @@ -7366,7 +7507,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -7628,6 +7769,116 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0043933", + "lbl" : "protein-containing complex organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.", + "xrefs" : [ "GOC:mah" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "protein complex subunit organisation", + "xrefs" : [ "GOC:mah" ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein complex subunit organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecular complex organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecular complex subunit organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecular complex subunit organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex subunit organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex subunit organization" + }, { + "pred" : "hasRelatedSynonym", + "val" : "protein-containing complex subunit organization" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22580" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "mah" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-09-08T10:01:42Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034600" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034621" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071822" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044085", + "lbl" : "cellular component biogenesis", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", + "xrefs" : [ "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular component biogenesis at cellular level" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0071843" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044207", + "lbl" : "translation initiation ternary complex", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).", + "xrefs" : [ "GOC:jl" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "translation initiation (ternary) complex" + }, { + "pred" : "hasNarrowSynonym", + "val" : "Met-tRNA/eIF2.GTP ternary complex" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "jl" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-10-22T02:38:55Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044237", "lbl" : "cellular metabolic process", @@ -7652,6 +7903,31 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0044238", + "lbl" : "primary metabolic process", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", + "xrefs" : [ "GOC:go_curators" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "primary metabolism" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26424" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0044249", "lbl" : "cellular biosynthetic process", @@ -8881,6 +9157,58 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0065003", + "lbl" : "protein-containing complex assembly", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.", + "xrefs" : [ "GOC:jl" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_pombe", "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cellular protein complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular macromolecule complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cellular protein-containing complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "chaperone activity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecular complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "macromolecule complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "protein complex assembly" + }, { + "pred" : "hasRelatedSynonym", + "val" : "protein complex formation" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/22580" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006461" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0034622" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0043623" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0065007", "lbl" : "biological regulation", @@ -8956,34 +9284,39 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_0071704", - "lbl" : "organic substance metabolic process", + "id" : "http://purl.obolibrary.org/obo/GO_0071826", + "lbl" : "protein-RNA complex organization", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.", + "val" : "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.", "xrefs" : [ "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolic process" + "val" : "RNA-protein complex subunit organization", + "xrefs" : [ "GOC:mah" ] + }, { + "pred" : "hasExactSynonym", + "val" : "protein-RNA complex subunit organization", + "xrefs" : [ "GOC:mah" ] }, { "pred" : "hasExactSynonym", - "val" : "organic molecular entity metabolism" + "val" : "ribonucleoprotein complex subunit organisation", + "xrefs" : [ "GOC:mah" ] }, { "pred" : "hasExactSynonym", - "val" : "organic substance metabolism" + "val" : "ribonucleoprotein complex subunit organization" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" + "val" : "https://github.com/geneontology/go-ontology/issues/25143" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "mah" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-03-08T03:32:18Z" + "val" : "2010-09-08T10:10:35Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" @@ -9652,62 +9985,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1902105", "lbl" : "regulation of leukocyte differentiation", @@ -9796,279 +10073,71 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/GO_2000026", - "lbl" : "regulation of multicellular organismal development", + "id" : "http://purl.obolibrary.org/obo/GO_1990904", + "lbl" : "ribonucleoprotein complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any process that modulates the frequency, rate or extent of multicellular organismal development.", - "xrefs" : [ "GOC:obol" ] + "val" : "A macromolecular complex that contains both RNA and protein molecules.", + "xrefs" : [ "GOC:krc", "GOC:vesicles" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "tb" + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "RNA-protein complex" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-08-05T11:25:59Z" + "pred" : "hasExactSynonym", + "val" : "RNP" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "pred" : "hasExactSynonym", + "val" : "protein-RNA complex" + }, { + "pred" : "hasNarrowSynonym", + "val" : "extracellular ribonucleoprotein complex" + }, { + "pred" : "hasNarrowSynonym", + "val" : "intracellular ribonucleoprotein complex" + } ], "xrefs" : [ { - "val" : "IAO:0000233" + "val" : "Wikipedia:Ribonucleoprotein" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pr" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2015-11-19T12:26:37Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0030529" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:1990903" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "cellular_component" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/GO_2000026", + "lbl" : "regulation of multicellular organismal development", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." + "val" : "Any process that modulates the frequency, rate or extent of multicellular organismal development.", + "xrefs" : [ "GOC:obol" ] }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "tb" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2010-08-05T11:25:59Z" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -10737,73 +10806,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -13411,6 +13413,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -13515,4893 +13541,6861 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." - }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "xrefs" : [ { - "val" : "RO:0000053" + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" + "val" : "protein" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000056" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000020", + "lbl" : "sense organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "An organ that is capable of transducing sensory stimulus to the nervous system.", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/549", "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "organ of sense organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory organ system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organ of sensory system", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sense organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory organ system organ", + "xrefs" : [ "OBOL:automatic" ] + }, { + "pred" : "hasExactSynonym", + "val" : "sensory system organ", + "xrefs" : [ "OBOL:accepted" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "sensillum", + "xrefs" : [ "WBbt:0006929" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Sinnesorgan", + "xrefs" : [ "BTO:0000202" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "sensor" + } ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "AEO:0000094" + }, { + "val" : "BSA:0000121" + }, { + "val" : "BTO:0000202" + }, { + "val" : "CALOHA:TS-2043" + }, { + "val" : "EHDAA2:0001824" + }, { + "val" : "EHDAA:500" + }, { + "val" : "EMAPA:35955" + }, { + "val" : "FBbt:00005155" + }, { + "val" : "GAID:63" + }, { + "val" : "HAO:0000930" + }, { + "val" : "MA:0000017" + }, { + "val" : "MESH:D012679" + }, { + "val" : "NCIT:C33224" + }, { + "val" : "SCTID:244485009" + }, { + "val" : "UMLS:C0935626" + }, { + "val" : "VHOG:0001407" + }, { + "val" : "WBbt:0006929" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], + "xrefs" : [ { + "val" : "galen:Tube" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000043", + "lbl" : "tendon", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "Dense regular connective tissue that connects muscle to bone[VSAO].", + "xrefs" : [ "GO_REF:0000034", "VSAO:0000073", "Wikipedia:Tendon", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "sinew", + "xrefs" : [ "Wikipedia:Tendon" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "tendo", + "xrefs" : [ "Wikipedia:Tendon" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000091" + }, { + "val" : "BTO:0001356" + }, { + "val" : "CALOHA:TS-1021" + }, { + "val" : "EHDAA2:0003091" + }, { + "val" : "EMAPA:35854" + }, { + "val" : "EV:0100149" + }, { + "val" : "FMA:9721" + }, { + "val" : "GAID:276" + }, { + "val" : "MA:0000115" + }, { + "val" : "MESH:D013710" + }, { + "val" : "NCIT:C13045" + }, { + "val" : "SCTID:256667004" + }, { + "val" : "UMLS:C0039508" + }, { + "val" : "VHOG:0001286" + }, { + "val" : "VSAO:0000073" + }, { + "val" : "Wikipedia:Tendon" + }, { + "val" : "XAO:0000173" + }, { + "val" : "ZFA:0005647" + }, { + "val" : "galen:Tendon" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "lbl" : "duct", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "A tubular structure that transports secreted or excreted substances.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165", "http://www.siumed.edu/~dking2/intro/glands.htm#ducts" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine gland duct" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "ducts", + "xrefs" : [ "XAO:0004000" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011123" + }, { + "val" : "FBbt:00100314" + }, { + "val" : "FMA:30320" + }, { + "val" : "NCIT:C12948" + }, { + "val" : "SCTID:91726008" + }, { + "val" : "TAO:0005171" + }, { + "val" : "UMLS:C0687028" + }, { + "val" : "Wikipedia:Duct_(anatomy)" + }, { + "val" : "XAO:0004000" + }, { + "val" : "ZFA:0005171" + }, { + "val" : "galen:Duct" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000060", + "lbl" : "anatomical wall", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.", + "xrefs" : [ "FMA:82482" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "wall" + }, { + "pred" : "hasExactSynonym", + "val" : "wall of organ", + "xrefs" : [ "FMA:82482" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ wall", + "xrefs" : [ "FMA:82482" ] + } ], + "xrefs" : [ { + "val" : "FMA:82482" + }, { + "val" : "galen:Wall" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0009915" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000061", + "lbl" : "anatomical structure", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.", + "xrefs" : [ "CARO:0000003" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "biological structure" + }, { + "pred" : "hasExactSynonym", + "val" : "connected biological structure", + "xrefs" : [ "CARO:0000003" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010825" + }, { + "val" : "AEO:0000003" + }, { + "val" : "BILA:0000003" + }, { + "val" : "CARO:0000003" + }, { + "val" : "EHDAA2:0003003" + }, { + "val" : "EMAPA:0" + }, { + "val" : "FBbt:00007001" + }, { + "val" : "FMA:305751" + }, { + "val" : "FMA:67135" + }, { + "val" : "GAID:781" + }, { + "val" : "HAO:0000003" + }, { + "val" : "MA:0003000" + }, { + "val" : "MESH:D000825" + }, { + "val" : "SCTID:362889002" + }, { + "val" : "TAO:0000037" + }, { + "val" : "TGMA:0001823" + }, { + "val" : "VHOG:0001759" + }, { + "val" : "XAO:0003000" + }, { + "val" : "ZFA:0000037" + }, { + "val" : "http://dbpedia.org/ontology/AnatomicalStructure" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001025", - "lbl" : "located in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000062", + "lbl" : "organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" + "val" : "Anatomical structure that performs a specific function or group of functions [WP].", + "xrefs" : [ "Wikipedia:Organ_(anatomy)" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "anatomical unit" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "hasRelatedSynonym", + "val" : "body organ" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Located_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", - "lbl" : "2D boundary of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" - }, + "pred" : "hasRelatedSynonym", + "val" : "element", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:4" + }, { + "val" : "CARO:0020004" + }, { + "val" : "EFO:0000634" + }, { + "val" : "EMAPA:35949" + }, { + "val" : "ENVO:01000162" + }, { + "val" : "FMA:67498" + }, { + "val" : "MA:0003001" + }, { + "val" : "NCIT:C13018" + }, { + "val" : "SCTID:272625005" + }, { + "val" : "UMLS:C0178784" + }, { + "val" : "WBbt:0003760" + }, { + "val" : "Wikipedia:Organ_(anatomy)" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", - "lbl" : "has 2D boundary", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000063", + "lbl" : "organ subunit", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + "val" : "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "organ region with fixed fiat boundary", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ segment", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "segment of organ", + "xrefs" : [ "FMA:86140" ] + } ], + "xrefs" : [ { + "val" : "FMA:86140" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002005", - "lbl" : "innervated_by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002006", - "lbl" : "has synaptic terminal of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002007", - "lbl" : "bounding layer of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000064", + "lbl" : "organ part", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. 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Cleavage ends with the formation of the blastula.", + "xrefs" : [ "GO:0040016", "Wikipedia:Cleavage_(embryo)" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000107" + }, { + "val" : "BilaDO:0000006" + }, { + "val" : "EFO:0001290" + }, { + "val" : "FBdv:00000054" + }, { + "val" : "MESH:D002970" + }, { + "val" : "MmusDv:0000004" + }, { + "val" : "OGES:000015" + }, { + "val" : "OGES:000020" + }, { + "val" : "PdumDv:0000200" + }, { + "val" : "Wikipedia:Cleavage_(embryo)" + }, { + "val" : "XAO:1000004" + }, { + "val" : "ZFS:0000046" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some Y?)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", - "lbl" : "overlaps", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000108", + "lbl" : "blastula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" + "val" : "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "xrefs" : [ { - "val" : "RO:0002131" + "val" : "BILS:0000108" + }, { + "val" : "BilaDO:0000007" + }, { + "val" : "EFO:0001282" + }, { + "val" : "HsapDv:0000006" + }, { + "val" : "MmusDv:0000007" + }, { + "val" : "OGES:000003" + }, { + "val" : "OGES:000016" + }, { + "val" : "OGES:000021" + }, { + "val" : "WBls:0000005" + }, { + "val" : "Wikipedia:Blastula" + }, { + "val" : "XAO:1000003" + }, { + "val" : "ZFS:0000045" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adding a preceding stage 'morula stage' as part of cleavage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002132", - "lbl" : "has fasciculating neuron projection", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002134", - "lbl" : "innervates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000109", + "lbl" : "gastrula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." + "val" : "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.", + "xrefs" : [ "GO:0007369" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blastocystis trilaminaris stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000109" + }, { + "val" : "BilaDO:0000008" + }, { + "val" : "EFO:0001296" + }, { + "val" : "FBdv:00005317" + }, { + "val" : "HsapDv:0000010" + }, { + "val" : "MmusDv:0000013" + }, { + "val" : "OGES:000004" + }, { + "val" : "OGES:000019" + }, { + "val" : "WBls:0000010" + }, { + "val" : "XAO:1000005" + }, { + "val" : "ZFS:0000047" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that ( some ( that some Y?)))" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002150", - "lbl" : "continuous with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000110", + "lbl" : "neurula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + "val" : "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.", + "xrefs" : [ "GO:0001841" ] }, + "xrefs" : [ { + "val" : "BILS:0000110" + }, { + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", - "lbl" : "shares ancestor with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." - }, - "comments" : [ "VBO calls this homologous_to" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", - "lbl" : "only in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000165", + "lbl" : "mouth", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." + "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).", + "xrefs" : [ "Wikipedia:Mouth", "https://github.com/obophenotype/uberon/wiki/The-digestive-tract" ] }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasExactSynonym", + "val" : "regio oralis", + "xrefs" : [ "BTO:0004698", "FMA:49184", "FMA:TA" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "adult mouth" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "cavital oralis", + "xrefs" : [ "Wikipedia:Mouth" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavitas oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "cavum oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth cavity", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral region", + "xrefs" : [ "EHDAA2:0001326" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral vestibule", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "rima oris", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "stoma" + }, { + "pred" : "hasRelatedSynonym", + "val" : "stomatodaeum", + "xrefs" : [ "VHOG:0000812" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trophic apparatus", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibule of mouth", + "xrefs" : [ "BTO:0001090" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vestibulum oris", + "xrefs" : [ "BTO:0001090" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010355" + }, { + "val" : "BTO:0001090" + }, { + "val" : "BTO:0004698" + }, { + "val" : "CALOHA:TS-1315" + }, { + "val" : "EFO:0000825" + }, { + "val" : "EHDAA2:0001326" + }, { + "val" : "EHDAA:542" + }, { + "val" : "EMAPA:16262" + }, { + "val" : "FBbt:00003126" + }, { + "val" : "FMA:49184" + }, { + "val" : "GAID:75" + }, { + "val" : "MA:0000341" + }, { + "val" : "MA:0002474" + }, { + "val" : "MAT:0000038" + }, { + "val" : "MESH:D009055" + }, { + "val" : "MIAA:0000038" + }, { + "val" : "SCTID:21082005" + }, { + "val" : "TADS:0000040" + }, { + "val" : "TAO:0000547" + }, { + "val" : "TAO:0000590" + }, { + "val" : "TGMA:0000131" + }, { + "val" : "VHOG:0000280" + }, { + "val" : "VHOG:0000812" + }, { + "val" : "Wikipedia:Mouth" + }, { + "val" : "XAO:0003029" + }, { + "val" : "ZFA:0000547" + }, { + "val" : "ZFA:0000590" + }, { + "val" : "galen:Mouth" + }, { + "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/uberon/issues/661" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000307", + "lbl" : "blastula", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "blastula embryo", + "xrefs" : [ "BILA:0000059" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "blastosphere", + "xrefs" : [ "Wikipedia:Blastula" ] + } ], + "xrefs" : [ { + "val" : "BILA:0000059" + }, { + "val" : "BTO:0000128" + }, { + "val" : "GAID:1294" + }, { + "val" : "MESH:D036703" + }, { + "val" : "OGEM:000006" + }, { + "val" : "Wikipedia:Blastula" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007011" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", + "lbl" : "musculature of body", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", + "xrefs" : [ "VSAO:0000033" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "muscle system" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" - }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + "pred" : "hasExactSynonym", + "val" : "muscle system of body" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." - }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "pred" : "hasExactSynonym", + "val" : "muscular system", + "xrefs" : [ "FMA:72954" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "pred" : "hasExactSynonym", + "val" : "musculature system", + "xrefs" : [ "BILA:0000088" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of all muscles", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "set of muscles of body", + "xrefs" : [ "FMA:72954" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate muscular system", + "xrefs" : [ "BTO:0001369" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "muskelsystem", + "xrefs" : [ "BTO:0001485" ] + } ], "xrefs" : [ { - "val" : "RO:0002180" + "val" : "AAO:0000307" + }, { + "val" : "BILA:0000088" + }, { + "val" : "BTO:0001369" + }, { + "val" : "BTO:0001485" + }, { + "val" : "EFO:0000801" + }, { + "val" : "FMA:72954" + }, { + "val" : "MA:0002888" + }, { + "val" : "MAT:0000025" + }, { + "val" : "MIAA:0000025" + }, { + "val" : "VSAO:0000033" + }, { + "val" : "XAO:0004042" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", + "lbl" : "organism substance", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "comments" : [ "TODO - add child relations from DOS" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "RO:0002211" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "body fluid or substance", + "xrefs" : [ "MA:0002450" ] }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "pred" : "hasExactSynonym", + "val" : "body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "organism substance", + "xrefs" : [ "CARO:0000004" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of body substance", + "xrefs" : [ "FMA:9669" ] + }, { + "pred" : "hasExactSynonym", + "val" : "portion of organism substance", + "xrefs" : [ "ZFA:0001487" ] + } ], "xrefs" : [ { - "val" : "RO:0002212" + "val" : "AAO:0010839" + }, { + "val" : "AEO:0000004" + }, { + "val" : "BILA:0000004" + }, { + "val" : "CALOHA:TS-2101" + }, { + "val" : "CARO:0000004" + }, { + "val" : "EHDAA2:0003004" + }, { + "val" : "EMAPA:35178" + }, { + "val" : "FBbt:00007019" + }, { + "val" : "FMA:9669" + }, { + "val" : "HAO:0000004" + }, { + "val" : "MA:0002450" + }, { + "val" : "NCIT:C13236" + }, { + "val" : "SPD:0000008" + }, { + "val" : "TAO:0001487" + }, { + "val" : "TGMA:0001824" + }, { + "val" : "VHOG:0001726" + }, { + "val" : "XAO:0004001" + }, { + "val" : "ZFA:0001487" + }, { + "val" : "galen:BodySubstance" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "negatively_regulates" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000464", + "lbl" : "anatomical space", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + "val" : "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "lumen" + }, { + "pred" : "hasBroadSynonym", + "val" : "space" + }, { + "pred" : "hasExactSynonym", + "val" : "lumen space" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "anatomical spaces", + "xrefs" : [ "ZFA:0001643" ] + } ], "xrefs" : [ { - "val" : "RO:0002213" + "val" : "AAO:0010110" + }, { + "val" : "AEO:0000005" + }, { + "val" : "BILA:0000005" + }, { + "val" : "CARO:0000005" + }, { + "val" : "EHDAA2:0003005" + }, { + "val" : "FBbt:00007017" + }, { + "val" : "FMA:5897" + }, { + "val" : "HAO:0000005" + }, { + "val" : "NCIT:C94478" + }, { + "val" : "TAO:0001668" + }, { + "val" : "TGMA:0001825" + }, { + "val" : "UMLS:C0524461" + }, { + "val" : "VHOG:0001728" + }, { + "val" : "XAO:0003190" + }, { + "val" : "ZFA:0001643" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "positively_regulates" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", + "lbl" : "material anatomical entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " + "val" : "Anatomical entity that has mass.", + "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0002215" + "val" : "AAO:0010264" + }, { + "val" : "AEO:0000006" + }, { + "val" : "BILA:0000006" + }, { + "val" : "CARO:0000006" + }, { + "val" : "EHDAA2:0003006" + }, { + "val" : "FBbt:00007016" + }, { + "val" : "FMA:67165" + }, { + "val" : "HAO:0000006" + }, { + "val" : "TAO:0001836" + }, { + "val" : "TGMA:0001826" + }, { + "val" : "VHOG:0001721" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - 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Here we take a cell type based approach." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "pred" : "hasExactSynonym", - "val" : "biological structure" + "val" : "muscular tissue" }, { "pred" : "hasExactSynonym", - "val" : "connected biological structure", - "xrefs" : [ "CARO:0000003" ] + "val" : "portion of muscle tissue", + "xrefs" : [ "FMA:9641" ] + }, { + "pred" : "hasExactSynonym", + "val" : "textus muscularis" } ], "xrefs" : [ { - "val" : "AAO:0010825" - }, { - "val" : "AEO:0000003" - }, { - "val" : "BILA:0000003" - }, { - "val" : "CARO:0000003" - }, { - "val" : "EHDAA2:0003003" - }, { - "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" - }, { - "val" : "FMA:305751" + "val" : "AAO:0000306" }, { - "val" : "FMA:67135" + "val" : "AEO:0000122" }, { - "val" : "GAID:781" + "val" : "CALOHA:TS-0642" }, { - "val" : "HAO:0000003" + "val" : "EHDAA2:0003122" }, { - "val" : "MA:0003000" + "val" : "EMAPA:32715" }, { - 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Bone is deposited by osteoblasts.", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000047", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "adult stage" + "pred" : "hasExactSynonym", + "val" : "calcium tissue" }, { "pred" : "hasExactSynonym", - "val" : "fully formed animal stage" + "val" : "osseous tissue" }, { "pred" : "hasExactSynonym", - "val" : "juvenile-adult stage" + "val" : "osteogenic tissue", + "xrefs" : [ "VSAO:curator" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "mineralized bone tissue", + "xrefs" : [ "XAO:0004040" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "bone", + "xrefs" : [ "MESH:A02.835.232" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "portion of bone tissue", + "xrefs" : [ "FMA:224804" ] } ], "xrefs" : [ { - "val" : "BTO:0001043" + "val" : "CALOHA:TS-2011" }, { - "val" : "BilaDO:0000004" + "val" : "EMAPA:35179" }, { - "val" : "EFO:0001272" + "val" : "FMA:224804" }, { - "val" : "FBdv:00005369" + "val" : "MA:0002780" + }, { + "val" : "MESH:D001842" + }, { + "val" : "NCIT:C13076" + }, { + "val" : "UMLS:C0391978" + }, { + "val" : "VSAO:0000047" + }, { + "val" : "Wikipedia:Bone_tissue" + }, { + "val" : "XAO:0004040" }, { - "val" : "WBls:0000041" + "val" : "ZFA:0005621" }, { - "val" : "XtroDO:0000084" + "val" : "galen:BoneTissue" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "see https://github.com/obophenotype/uberon/issues/27" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/566" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000068", - "lbl" : "embryo stage", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002530", + "lbl" : "gland", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A life cycle stage that starts with fertilization and ends with the fully formed embryo.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "An organ that functions as a secretory or excretory organ.", + "xrefs" : [ "MGI:csmith", "MP:0002163" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "embryonic stage" + "val" : "glandular organ", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasRelatedSynonym", - "val" : "embryogenesis" + "val" : "Druese", + "xrefs" : [ "BTO:0000522" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "glandula", + "xrefs" : [ "BTO:0000522", "Wikipedia:Gland" ] } ], "xrefs" : [ { - "val" : "BilaDO:0000002" + "val" : "AAO:0000212" }, { - "val" : "EV:0300001" + "val" : "AEO:0000096" }, { - "val" : "FBdv:00005289" + "val" : "BTO:0000522" }, { - "val" : "FMA:72652" + "val" : "EFO:0000797" }, { - "val" : "HsapDv:0000002" + "val" : "EHDAA2:0003096" }, { - "val" : "MmusDv:0000002" + "val" : "EHDAA:2161" }, { - "val" : "OGES:000000" + "val" : "EMAPA:18425" }, { - "val" : "OGES:000022" + "val" : "FBbt:00100317" }, { - "val" : "SCTID:296280003" + "val" : "FMA:7146" }, { - "val" : "WBls:0000003" + "val" : "FMA:86294" }, { - "val" : "WBls:0000092" + "val" : "HAO:0000375" }, { - "val" : "WBls:0000102" + "val" : "MA:0003038" }, { - "val" : "XAO:1000012" + "val" : "MAT:0000021" + }, { + "val" : "MIAA:0000021" + }, { + "val" : "NCIT:C13319" + }, { + "val" : "SCTID:134358001" + }, { + "val" : "UMLS:C1285092" + }, { + "val" : "Wikipedia:Gland" + }, { + "val" : "WikipediaCategory:Glands" + }, { + "val" : "galen:Gland" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000071", - "lbl" : "death stage", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", + "lbl" : "epiblast (generic)", "type" : "CLASS", "meta" : { "definition" : { - "val" : "End of the life of an organism.", - "xrefs" : [ "XAO:0000437" ] + "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. 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This will give rise to the central nervous system.", - "xrefs" : [ "GO:0001841" ] - }, - "xrefs" : [ { - "val" : "BILS:0000110" + "val" : "NCIT:C34214" }, { - "val" : "BilaDO:0000009" + "val" : "SCTID:344535001" }, { - "val" : "HsapDv:0000012" + "val" : "TAO:0001056" }, { - "val" : "MmusDv:0000017" + "val" : "UMLS:C1513802" }, { - "val" : "XAO:1000006" + "val" : "VHOG:0001244" + }, { + "val" : "Wikipedia:Myotome" + }, { + "val" : "XAO:0000315" + }, { + "val" : "ZFA:0001056" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/343" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "lbl" : "organogenesis stage", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", + "lbl" : "compound organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", - "xrefs" : [ "Wikipedia:Organogenesis" ] + "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", + "xrefs" : [ "CARO:0000024" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "segmentation stage" + "val" : "organ" } ], "xrefs" : [ { - "val" : "BILS:0000111" + "val" : "AAO:0010015" }, { - "val" : "BilaDO:0000010" + "val" : "AEO:0000024" }, { - "val" : "HsapDv:0000015" + "val" : "BILA:0000024" }, { - "val" : "MmusDv:0000018" + "val" : "CARO:0000024" }, { - "val" : "OGES:000005" + "val" : "EHDAA2:0003024" }, { - "val" : "OGES:000032" + "val" : "HAO:0000024" }, { - "val" : "Wikipedia:Organogenesis" + "val" : "TADS:0000598" + }, { + "val" : "TAO:0000496" + }, { + "val" : "TGMA:0001837" + }, { + "val" : "VHOG:0001723" + }, { + "val" : "XAO:0003041" + }, { + "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "lbl" : "mouth", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", + "lbl" : "mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. 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See https://github.com/obophenotype/uberon/issues/77" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004120", + "lbl" : "mesoderm-derived structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - 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This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000467", - "lbl" : "anatomical system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", + "lbl" : "gastrula", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.", - "xrefs" : [ "CARO:0000011" ] + "val" : "Organism at the gastrula stage.", + "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "system", - "xrefs" : [ "GO:0048731" ] - }, { - "pred" : "hasExactSynonym", - "val" : "body system", - "xrefs" : [ "BIRNLEX:14" ] - }, { - "pred" : "hasExactSynonym", - "val" : "connected anatomical system", - "xrefs" : [ "CARO:0000011" ] - }, { "pred" : "hasExactSynonym", - "val" : "organ system" + "val" : "gastrula embryo", + "xrefs" : [ "BILA:0000060" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "anatomical systems", - "xrefs" : [ "ZFA:0001439" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000007" - }, { - "val" : "AEO:0000011" + "val" : "blastocystis trilaminaris", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "BILA:0000011" + "pred" : "hasRelatedSynonym", + "val" : "tri-laminar disc", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "BIRNLEX:14" + "pred" : "hasRelatedSynonym", + "val" : "tri-laminar disk", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "BSA:0000049" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "CALOHA:TS-2088" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "CARO:0000011" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disc", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "EHDAA2:0003011" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "EHDAA:392" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILA:0000060" }, { - "val" : "EMAPA:16103" + "val" : "BTO:0001403" }, { - "val" : "EV:0100000" + "val" : "FBbt:00005317" }, { - "val" : "FBbt:00004856" + "val" : "FMA:293108" }, { - "val" : "FMA:7149" + "val" : "GAID:1302" }, { - "val" : "HAO:0000011" + "val" : "MESH:D005775" }, { - "val" : "MA:0000003" + "val" : "MIAA:0000179" }, { - "val" : "NCIT:C12919" + "val" : "NCIT:C34057" }, { - "val" : "SCTID:278195005" + "val" : "NCIT:C34058" }, { - "val" : "TAO:0001439" + "val" : "UMLS:C0017199" }, { - "val" : "TGMA:0001831" + "val" : "UMLS:C1284022" }, { - "val" : "UMLS:C0460002" + "val" : "Wikipedia:Gastrula" }, { - "val" : "VHOG:0001725" + "val" : "Wikipedia:Trilaminar_blastocyst" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007012" }, { - "val" : "WBbt:0005746" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004755", + "lbl" : "skeletal tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000015", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/134" ] + }, + "comments" : [ "Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from" ], + "xrefs" : [ { + "val" : "EMAPA:37744" }, { - "val" : "WBbt:0005763" + "val" : "MA:0003047" }, { - "val" : "Wikipedia:Organ_system" + "val" : "SCTID:309311006" }, { - "val" : "XAO:0003002" + "val" : "VSAO:0000015" }, { - "val" : "ZFA:0001439" + "val" : "XAO:0004038" }, { - "val" : "galen:AnatomicalSystem" + "val" : "ZFA:0005619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", + "lbl" : "skeletal element", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "AAO:0011129" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "val" : "TAO:0001890" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "VSAO:0000128" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "XAO:0004012" + }, { + "val" : "ZFA:0005494" }, { + "val" : "galen:SkeletalStructure" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/EHDAA2_0001330" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "lbl" : "multicellular organism", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", + "lbl" : "articular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that is an individual member of a species and consists of more than one cell.", - "xrefs" : [ "CARO:0000012", "Wikipedia:Multi-cellular_organism", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Anatomical system that consists of all the joints of the body.", + "xrefs" : [ "VSAO:0000181" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "organism", - "xrefs" : [ "FBbt:00000001", "VHOG:0000671", "WBbt:0007833" ] - }, { "pred" : "hasExactSynonym", - "val" : "multi-cellular organism", - "xrefs" : [ "CARO:0000012" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Koerper", - "xrefs" : [ "BTO:0001489" ] + "val" : "joint system", + "xrefs" : [ "FMA:23878" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "body", - "xrefs" : [ "AEO:0000103", "BIRNLEX:18", "FMA:256135", "NCIT:C13041" ] + "pred" : "hasExactSynonym", + "val" : "set of all joints of body", + "xrefs" : [ "FMA:23878" ] }, { "pred" : "hasRelatedSynonym", - "val" : "whole body", - "xrefs" : [ "BTO:0001489" ] + "val" : "set of all joints" }, { "pred" : "hasRelatedSynonym", - "val" : "whole organism", - "xrefs" : [ "FBbt:00000001" ] + "val" : "set of joints of body", + "xrefs" : [ "FMA:23878" ] } ], "xrefs" : [ { - "val" : "AAO:0010026" - }, { - "val" : "AEO:0000191" - }, { - "val" : "BILA:0000012" - }, { - "val" : "BIRNLEX:18" - }, { - "val" : "BSA:0000038" - }, { - "val" : "BTO:0000042" - }, { - "val" : "CARO:0000012" - }, { - "val" : "EFO:0002906" - }, { - "val" : "EHDAA2:0003103" - }, { - "val" : "EHDAA2:0003191" - }, { - "val" : "EHDAA:1" - }, { - "val" : "EMAPA:25765" - }, { - "val" : "EV:0100016" + "val" : "EMAPA:35150" }, { - "val" : "FBbt:00000001" + "val" : "FMA:23878" }, { - "val" : "FMA:256135" + "val" : "MA:0003007" }, { - "val" : "HAO:0000012" + "val" : "SCTID:361827000" }, { - "val" : "NCIT:C13041" + "val" : "VSAO:0000181" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", + "lbl" : "chordamesoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The central region of trunk mesoderm. 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"xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "One of the two elevated edges of the neural groove[GO,MP].", + "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "acellular anatomical structures", - "xrefs" : [ "ZFA:0000382" ] + "pred" : "hasExactSynonym", + "val" : "medullary fold", + "xrefs" : [ "MP:0011256" ] } ], "xrefs" : [ { - "val" : "AAO:0010268" - }, { - "val" : "AEO:0000040" - }, { - "val" : "BILA:0000040" - }, { - "val" : "CARO:0000040" - }, { - "val" : "EHDAA2:0003040" + "val" : "EHDAA2:0001249" }, { - "val" : "FBbt:00007013" + "val" : "FMA:295618" }, { - "val" : "FMA:63863" + "val" : "NCIT:C34223" }, { - "val" : "HAO:0000040" + "val" : "SCTID:361461009" }, { - "val" : "TAO:0000382" + "val" : "UMLS:C0814993" }, { - "val" : "TGMA:0001841" + "val" : "Wikipedia:Neural_fold" }, { - "val" : "XAO:0003162" + "val" : "XAO:0004087" }, { - "val" : "ZFA:0000382" + "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000477", - "lbl" : "anatomical cluster", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005068", + "lbl" : "neural rod", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical group whose component anatomical structures lie in close proximity to each other.", - "xrefs" : [ "FBbt:00007277" ] + "val" : "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].", + "xrefs" : [ "GO:0014024", "ZFA:0000133" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "neural tube rod", + "xrefs" : [ "GO:0014027" ] + } ], "xrefs" : [ { - "val" : "FBbt:00007277" + "val" : "EFO:0003498" }, { - "val" : "VHOG:0001737" + "val" : "TAO:0000133" + }, { + "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000478", - "lbl" : "extraembryonic structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", + "lbl" : "muscle structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.", - "xrefs" : [ "CARO:DOS", "http://orcid.org/0000-0001-9114-8737", "https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279" ] + "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", + "xrefs" : [ "GO:0061061" ] }, - "comments" : [ "see also conceptus extraembryonic component in EHDAA2." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "extra-embryonic structure" + "val" : "musculus", + "xrefs" : [ "FMA:30316" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "extraembryonic structures", - "xrefs" : [ "ZFA:0000020" ] + "val" : "muscle" }, { "pred" : "hasRelatedSynonym", - "val" : "extraembryonic tissue" + "val" : "muscle element" } ], "xrefs" : [ { - "val" : "AAO:0010020" - }, { - "val" : "AEO:0000042" - }, { - "val" : "BILA:0000042" - }, { - "val" : "CALOHA:TS-2119" - }, { - "val" : "CARO:0000042" - }, { - "val" : "EHDAA2:0003042" - }, { - "val" : "EHDAA:46" - }, { - "val" : "FBbt:00005835" - }, { - "val" : "FMA:85537" - }, { - "val" : "HAO:0000042" - }, { - "val" : "NCIT:C34055" - }, { - "val" : "SCTID:314908006" + "val" : "FMA:30316" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", + "lbl" : "epithelial fold", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelial sheet bent on a linear axis.", + "xrefs" : [ "GO:0060571" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005256", + "lbl" : "trunk mesenchyme", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mesenchyme that is part of a developing trunk.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "trunk and cervical mesenchyme", + "xrefs" : [ "EHDAA2:0002092" ] + } ], + "xrefs" : [ { + "val" : "EFO:0003485" }, { - "val" : "TAO:0000020" + "val" : "EHDAA2:0002092" }, { - "val" : "TGMA:0001843" + "val" : "EHDAA:377" }, { - "val" : "UMLS:C1282438" + "val" : "EMAPA:16177" }, { - "val" : "VHOG:0000292" + "val" : "TAO:0000081" }, { - "val" : "XAO:0004005" + "val" : "VHOG:0000281" }, { - "val" : "ZFA:0000020" + "val" : "ZFA:0000081" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18409,78 +20403,83 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000479", - "lbl" : "tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005291", + "lbl" : "embryonic tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.", - "xrefs" : [ "CARO:0000043" ] + "val" : "A portion of tissue that is part of an embryo.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "portion of tissue", - "xrefs" : [ "CARO:0000043" ] + "val" : "portion of embryonic tissue", + "xrefs" : [ "OBOL:automatic" ] }, { + "pred" : "hasRelatedSynonym", + "val" : "developing tissue" + } ], + "xrefs" : [ { + "val" : "CALOHA:TS-2100" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005388", + "lbl" : "photoreceptor array", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An array of photoreceptors and any supporting cells found in an eye.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "tissue portion" - }, { - "pred" : "hasNarrowSynonym", - "val" : "simple tissue", - "xrefs" : [ "AEO:0000043" ] + "val" : "light-sensitive tissue" } ], "xrefs" : [ { - "val" : "AAO:0000607" - }, { - "val" : "AAO:0010054" - }, { - "val" : "AEO:0000043" - }, { - "val" : "BILA:0000043" - }, { - "val" : "BIRNLEX:19" - }, { - "val" : "CALOHA:TS-2090" - }, { - "val" : "CARO:0000043" - }, { - "val" : "EHDAA2:0003043" - }, { - "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" - }, { - "val" : "FMA:9637" - }, { - "val" : "HAO:0000043" - }, { - "val" : "MA:0003002" - }, { - "val" : "MESH:D014024" - }, { - "val" : "NCIT:C12801" - }, { - "val" : "TAO:0001477" + "val" : "FBbt:00004200" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005423", + "lbl" : "developing anatomical structure", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "developing structure" }, { - "val" : "TGMA:0001844" + "pred" : "hasRelatedSynonym", + "val" : "developmental structure" }, { - "val" : "UMLS:C0040300" + "pred" : "hasRelatedSynonym", + "val" : "developmental tissue", + "xrefs" : [ "MIAA:0000019" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000125" }, { - "val" : "VHOG:0001757" + "val" : "CALOHA:TS-2122" }, { - "val" : "WBbt:0005729" + "val" : "EHDAA2:0003125" }, { - "val" : "XAO:0003040" + "val" : "FBbt:00007006" }, { - "val" : "ZFA:0001477" + "val" : "FMA:292313" }, { - "val" : "galen:Tissue" + "val" : "MIAA:0000019" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "changed label and definition to reflect CARO2" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -18495,45 +20494,17 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000481", - "lbl" : "multi-tissue structure", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005764", + "lbl" : "acellular membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.", - "xrefs" : [ "CARO:0000055", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "An acellular anatomical structure that is the bounding layer of a anatomical structure.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "multi-tissue structures", - "xrefs" : [ "ZFA:0001488" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { - "val" : "AAO:0010048" - }, { - "val" : "AEO:0000055" - }, { - "val" : "BILA:0000055" - }, { - "val" : "CARO:0000055" - }, { - "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" - }, { - "val" : "HAO:0000055" - }, { - "val" : "TAO:0001488" - }, { - "val" : "TGMA:0001847" - }, { - "val" : "VHOG:0001762" - }, { - "val" : "XAO:0003037" - }, { - "val" : "ZFA:0001488" + "val" : "FMA:63871" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -18550,127 +20521,138 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "lbl" : "epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "lbl" : "basement membrane of epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].", - "xrefs" : [ "Wikipedia:Epithelium", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.", + "xrefs" : [ "Wikipedia:Basement_membrane", "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "epithelial tissue" + "val" : "basement membrane of connective tissue", + "xrefs" : [ "FMA:63872" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "portion of epithelium", - "xrefs" : [ "FMA:9639" ] + "val" : "membrana basalis", + "xrefs" : [ "Wikipedia:Basement_membrane" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "basement membrane", + "xrefs" : [ "FMA:63872" ] } ], "xrefs" : [ { - "val" : "AAO:0000144" - }, { - "val" : "AAO:0010055" - }, { - "val" : "AEO:0000066" - }, { - "val" : "BILA:0000066" - }, { - "val" : "BTO:0000416" - }, { - "val" : "CALOHA:TS-0288" - }, { - "val" : "CARO:0000066" - }, { - "val" : "EHDAA2:0003066" - }, { - "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" - }, { - "val" : "FMA:9639" + "val" : "AAO:0010596" }, { - "val" : "GAID:402" + "val" : "FMA:63872" }, { - "val" : "HAO:0000066" + "val" : "GAID:915" }, { - "val" : "MA:0003060" + "val" : "NCIT:C13191" }, { - "val" : "MESH:D004848" + "val" : "SCTID:68989006" }, { - "val" : "NCIT:C12710" + "val" : "UMLS:C0004799" }, { - "val" : "SCTID:31610004" + "val" : "Wikipedia:Basement_membrane" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { - "val" : "TAO:0001486" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", + "lbl" : "notochordal plate", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", + "xrefs" : [ "VHOG:0001212" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], + "xrefs" : [ { + "val" : "EHDAA2:0001278" }, { - "val" : "UMLS:C0014609" + "val" : "EHDAA:264" }, { - "val" : "VHOG:0000387" + "val" : "EMAPA:16101" }, { - "val" : "Wikipedia:Epithelium" + "val" : "NCIT:C34231" }, { - "val" : "XAO:0003045" + "val" : "UMLS:C1518429" }, { - "val" : "ZFA:0001486" + "val" : "VHOG:0001212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ordering; awaiting confirmation from JB" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000486", - "lbl" : "multilaminar epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", + "lbl" : "notochordal process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA].", - "xrefs" : [ "FMA:FMA", "Wikipedia:Stratified_epithelium", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", + "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "stratified epithelium" + "pred" : "hasRelatedSynonym", + "val" : "chordamesoderm" }, { "pred" : "hasRelatedSynonym", - "val" : "laminated epithelium", - "xrefs" : [ "BTO:0002074" ] + "val" : "presumptive notochord" } ], "xrefs" : [ { - "val" : "AAO:0010059" - }, { - "val" : "AEO:0000069" - }, { - "val" : "BILA:0000069" - }, { - "val" : "BTO:0002074" - }, { - "val" : "CARO:0000069" - }, { - "val" : "EHDAA2:0003069" + "val" : "EHDAA2:0001279" }, { - "val" : "FMA:45562" + "val" : "EHDAA:224" }, { - "val" : "HAO:0000069" + "val" : "EMAPA:16102" }, { - "val" : "NCIT:C33622" + "val" : "FMA:293135" }, { - "val" : "SCTID:309044005" + "val" : "NCIT:C34232" }, { - "val" : "TAO:0001494" + "val" : "UMLS:C1518430" }, { - "val" : "UMLS:C0682575" + "val" : "VHOG:0001213" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006595", + "lbl" : "presumptive endoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Presumptive structure of the blastula that will develop into endoderm.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "AAO:0000471" }, { - "val" : "Wikipedia:Stratified_epithelium" + "val" : "EFO:0003437" }, { - "val" : "XAO:0004006" + "val" : "TAO:0000416" }, { - "val" : "ZFA:0001494" + "val" : "ZFA:0000416" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18678,212 +20660,207 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000490", - "lbl" : "unilaminar epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006598", + "lbl" : "presumptive structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].", - "xrefs" : [ "FMA:45561", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Portion of embryonic tissue determined by fate mapping to become a structure.", + "xrefs" : [ "GOC:CVS", "GOC:YMB", "ZFA:0001116" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "simple epithelium", - "xrefs" : [ "FMA:45561" ] + "val" : "future structure" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "unilaminar epithelia", - "xrefs" : [ "ZFA:0001495" ] + "pred" : "hasExactSynonym", + "val" : "presumptive structures", + "xrefs" : [ "ZFA:0001116" ] } ], "xrefs" : [ { - "val" : "AAO:0010062" - }, { - "val" : "AEO:0000073" - }, { - "val" : "BILA:0000073" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000073" - }, { - "val" : "EHDAA2:0003073" - }, { - "val" : "FMA:45561" - }, { - "val" : "HAO:0000073" - }, { - "val" : "NCIT:C33554" - }, { - "val" : "SCTID:309043004" - }, { - "val" : "TAO:0001495" - }, { - "val" : "UMLS:C0682574" + "val" : "AAO:0000479" }, { - "val" : "XAO:0004007" + "val" : "TAO:0001116" }, { - "val" : "ZFA:0001495" + "val" : "ZFA:0001116" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" + "val" : "Consider merging with anlage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000922", - "lbl" : "embryo", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006601", + "lbl" : "presumptive ectoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.", - "xrefs" : [ "BTO:0000379", "FB:FBrf0039741", "FB:FBrf0041814", "GO:0009790", "Wikipedia:Embryo" ] + "val" : "Presumptive structure of the blastula that will develop into ectoderm.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic organism", - "xrefs" : [ "BILA:0000056" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing organism", - "xrefs" : [ "BILA:0000056" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "developmental tissue" + "val" : "presumptive epidermis", + "xrefs" : [ "ZFA:0001376" ] } ], "xrefs" : [ { - "val" : "AAO:0011035" - }, { - "val" : "AEO:0000169" - }, { - "val" : "BILA:0000056" - }, { - "val" : "BSA:0000039" - }, { - "val" : "BTO:0000379" + "val" : "AAO:0000470" }, { - "val" : "CALOHA:TS-0229" + "val" : "EFO:0003466" }, { - "val" : "EFO:0001367" + "val" : "TAO:0001376" }, { - "val" : "EHDAA2:0000002" + "val" : "XAO:0004132" }, { - "val" : "EHDAA2_RETIRED:0003236" + "val" : "ZFA:0001376" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006603", + "lbl" : "presumptive mesoderm", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Presumptive structure of the blastula that will develop into mesoderm.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "AAO:0000476" }, { - "val" : "EHDAA:38" + "val" : "EFO:0003467" }, { - "val" : "EMAPA:16039" + "val" : "TAO:0001377" }, { - "val" : "FBbt:00000052" + "val" : "ZFA:0001377" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006984", + "lbl" : "anatomical surface", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] + }, + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "BILA:0000010" }, { - "val" : "FMA:69068" + "val" : "CARO:0001002" }, { - "val" : "GAID:963" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "MAT:0000226" + "val" : "FMA:24137" }, { - "val" : "MESH:D004622" + "val" : "NCIT:C34022" }, { - "val" : "MIAA:0000019" + "val" : "UMLS:C1515977" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", + "lbl" : "cleaving embryo", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Organism at the cleavage stage.", + "xrefs" : [ "OBOL:automatic" ] + }, + "xrefs" : [ { + "val" : "BILA:0000058" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", + "lbl" : "presumptive gut", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "future digestive tract" }, { - "val" : "NCIT:C28147" + "pred" : "hasExactSynonym", + "val" : "future digestive tube" }, { - "val" : "OGEM:000001" + "pred" : "hasExactSynonym", + "val" : "future gut" }, { - "val" : "SCTID:57991002" + "pred" : "hasExactSynonym", + "val" : "primitive gut" }, { - "val" : "UMLS:C0013935" + "pred" : "hasRelatedSynonym", + "val" : "embryonic digestive tube" }, { - "val" : "VHOG:0001766" + "pred" : "hasRelatedSynonym", + "val" : "primordial digestive tube" }, { - "val" : "Wikipedia:Embryo" + "pred" : "hasRelatedSynonym", + "val" : "primordial gut" + } ], + "xrefs" : [ { + "val" : "BILA:0000084" }, { - "val" : "XAO:0000113" + "val" : "NCIT:C34268" }, { - "val" : "ZFA:0000103" + "val" : "SCTID:360394002" }, { - "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" + "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/503" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "lbl" : "germ layer", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007100", + "lbl" : "primary circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.", - "xrefs" : [ "Wikipedia:Germ_layer", "https://github.com/obophenotype/uberon/issues/203" ] + "val" : "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].", + "xrefs" : [ "GO:0007507" ] }, - "comments" : [ "Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "Gene notes: Bmp, Nkx, Gata" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "embryonic tissue", - "xrefs" : [ "FMA:69069" ] - }, { - "pred" : "hasExactSynonym", - "val" : "germinal layer", - "xrefs" : [ "ncithesaurus:Germinal_Layer" ] - }, { "pred" : "hasNarrowSynonym", - "val" : "primary germ layer", - "xrefs" : [ "GO:0001704", "ZFA:0001122" ] + "val" : "dorsal tube", + "xrefs" : [ "Wikipedia:Heart" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layer" + "pred" : "hasNarrowSynonym", + "val" : "heart", + "xrefs" : [ "GO:0007507" ] }, { "pred" : "hasRelatedSynonym", - "val" : "embryonic germ layers" + "val" : "adult heart", + "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "AAO:0000480" - }, { - "val" : "BILA:0000035" - }, { - "val" : "BTO:0000556" - }, { - "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" - }, { - "val" : "FMA:69069" - }, { - "val" : "GAID:1303" - }, { - "val" : "MESH:D005855" - }, { - "val" : "NCIT:C12950" - }, { - "val" : "NCIT:C54105" - }, { - "val" : "TAO:0001122" - }, { - "val" : "UMLS:C0920502" - }, { - "val" : "UMLS:C1708239" - }, { - "val" : "VHOG:0001223" - }, { - "val" : "Wikipedia:Germ_layer" - }, { - "val" : "XAO:0003011" + "val" : "TADS:0000147" }, { - "val" : "ZFA:0001122" + "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18891,371 +20868,276 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", - "lbl" : "ectoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007135", + "lbl" : "neural keel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", - "xrefs" : [ "Wikipedia:Ectoderm" ] + "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.", + "xrefs" : [ "ZFIN:ZDB-PUB-961014-576" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryonic ectoderm", - "xrefs" : [ "VHOG:0000153" ] + "pred" : "hasRelatedSynonym", + "val" : "presumptive central nervous system", + "xrefs" : [ "ZFA:0000131" ] } ], "xrefs" : [ { - "val" : "AAO:0000137" - }, { - "val" : "BILA:0000036" - }, { - "val" : "BTO:0000315" - }, { - "val" : "CALOHA:TS-0216" - }, { - 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"val" : "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.", - "xrefs" : [ "Wikipedia:Endoderm" ] + "val" : "A presumptive structure that has the potential to develop into a presomitic mesoderm.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "entoderm", - "xrefs" : [ "DOI:10.5962/bhl.title.1013" ] + "val" : "presumptive segmental plates", + "xrefs" : [ "ZFA:0000053" ] } ], "xrefs" : [ { - "val" : "AAO:0000139" - }, { - "val" : "BILA:0000038" - 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"val" : "VHOG:0000154" + "pred" : "hasExactSynonym", + "val" : "future paraxial mesoderm" + } ], + "xrefs" : [ { + "val" : "EFO:0003443" }, { - "val" : "Wikipedia:Endoderm" + "val" : "TAO:0000591" }, { - "val" : "XAO:0000090" + "val" : "XAO:0004134" }, { - "val" : "ZFA:0000017" + "val" : "ZFA:0000591" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "lbl" : "mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007503", + "lbl" : "epithelial vesicle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The middle germ layer of the embryo, between the endoderm and ectoderm.", - "xrefs" : [ "Wikipedia:Mesoderm" ] + "val" : "A closed epithelium with a lumen.", + "xrefs" : [ "AEO:JB" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "embryonic mesoderm", - "xrefs" : [ "VHOG:0000152" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "entire mesoderm", - "xrefs" : [ "SCTID:362854004", "https://orcid.org/0000-0002-6601-2165" ] + "xrefs" : [ { + "val" : "AEO:0000119" }, { - "pred" : "hasRelatedSynonym", - "val" : "mesodermal mantle" + "val" : "EHDAA2:0003119" } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007524", + "lbl" : "dense mesenchyme tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mesenchyme with little extracellular matrix.", + "xrefs" : [ "AEO:JB" ] + }, "xrefs" : [ { - "val" : "AAO:0000304" - }, { - "val" : "BILA:0000037" - }, { - "val" : "BTO:0000839" - }, { - "val" : "CALOHA:TS-0623" - }, { - "val" : "EFO:0001981" - }, { - "val" : "EHDAA2:0001128" - }, { - "val" : "EHDAA:124" - }, { - "val" : "EHDAA:160" - }, { - "val" : "EHDAA:183" - }, { - "val" : "EMAPA:16083" - }, { - "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" - }, { - "val" : "FMA:69072" - }, { - "val" : "GAID:522" - }, { - "val" : "MAT:0000174" - }, { - "val" : "MESH:D008648" - }, { - "val" : "MIAA:0000174" - }, { - "val" : "NCIT:C12750" - }, { - "val" : "SCTID:362854004" - }, { - "val" : "TAO:0000041" - }, { - "val" : "UMLS:C0025485" - }, { - "val" : "VHOG:0000152" - }, { - "val" : "Wikipedia:Mesoderm" - }, { - "val" : "XAO:0000050" + "val" : "AEO:0000146" }, { - "val" : "ZFA:0000041" + "val" : "EHDAA2:0003146" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007845", + "lbl" : "regular connective tissue", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.", + "xrefs" : [ "FMA:20103" ] + }, + "xrefs" : [ { + "val" : "FMA:20103" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "lbl" : "stomodeum", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007846", + "lbl" : "dense regular connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.", - "xrefs" : [ "Wikipedia:Stomodeum", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/326" ] + "val" : "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000050", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "stomodeal-hypophyseal primordium", - "xrefs" : [ "XAO:0000269" ] - }, { "pred" : "hasExactSynonym", - "val" : "mouth primordium", - "xrefs" : [ "XAO:0000269" ] + "val" : "dense fibrous connective tissue", + "xrefs" : [ "FMA:64781" ] }, { "pred" : "hasExactSynonym", - "val" : "primitive oral cavity", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "dense regular collagenous connective tissue", + "xrefs" : [ "FMA:64781" ] }, { "pred" : "hasExactSynonym", - "val" : "stomatodeum", - "xrefs" : [ "Wikipedia:Stomodeum" ] + "val" : "dense regular collagenous tissue", + "xrefs" : [ "FMA:64781" ] }, { "pred" : "hasExactSynonym", - "val" : "stomodaeum" - }, { - "pred" : "hasRelatedSynonym", - "val" : "mouth pit", - "xrefs" : [ "EMAPA:16263" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "oral ectoderm", - "xrefs" : [ "ZFA:0001290", "ZFIN:ZDB-PUB-100726-23" ] + "val" : "regular dense connective tissue" }, { - "pred" : "hasRelatedSynonym", - "val" : "oral pit", - "xrefs" : [ "EMAPA:16263" ] + "pred" : "hasExactSynonym", + "val" : "typus regularis (textus connectivus collagenosus compactus)", + "xrefs" : [ "FMA:64781" ] } ], "xrefs" : [ { - "val" : "BTO:0004224" - }, { - "val" : "EHDAA2:0001929" - }, { - "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" + "val" : "FMA:64781" }, { - "val" : "FMA:295846" + "val" : "NCIT:C33453" }, { - "val" : "NCIT:C34306" + "val" : "SCTID:22560007" }, { - "val" : "TAO:0001290" + "val" : "UMLS:C0225333" }, { - "val" : "TGMA:0000135" + "val" : "VSAO:0000050" }, { - "val" : "UMLS:C1514977" + "val" : "Wikipedia:Dense_regular_connective_tissue" }, { - "val" : "Wikipedia:Stomodeum" + "val" : "XAO:0004030" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", + "lbl" : "entire embryonic mesenchyme", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Sum total of mesenchyme in the embryo.", + "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] + }, + "xrefs" : [ { + "val" : "EHDAA2:0001113" }, { - "val" : "XAO:0000269" + "val" : "EHDAA:177" }, { - "val" : "ZFA:0001290" + "val" : "EMAPA:16097" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" + "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003313" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000949", - "lbl" : "endocrine system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", + "lbl" : "trunk paraxial mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.", - "xrefs" : [ "NLM:endocrine+system", "Wikipedia:Endocrine_system" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "endocrine glandular system", - "xrefs" : [ "EHDAA2:0002224" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocrine system" + "val" : "trunk and cervical paraxial mesenchyme", + "xrefs" : [ "EHDAA2:0002094" ] }, { - "pred" : "hasExactSynonym", - "val" : "systema endocrinum" + "pred" : "hasRelatedSynonym", + "val" : "trunk paraxial mesenchyme", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] } ], "xrefs" : [ { - "val" : "AAO:0010279" - }, { - "val" : "CALOHA:TS-1301" - }, { - "val" : "EFO:0002969" - }, { - "val" : "EHDAA2:0002224" - }, { - "val" : "EMAPA:35306" - }, { - "val" : "EV:0100128" - }, { - "val" : "FBbt:00005068" - }, { - "val" : "FMA:9668" - }, { - "val" : "GAID:439" - }, { - "val" : "MA:0000012" - }, { - "val" : "MESH:D004703" - }, { - "val" : "NCIT:C12705" - }, { - "val" : "SCTID:278876000" - }, { - "val" : "TAO:0001158" - }, { - "val" : "UMLS:C0014136" - }, { - "val" : "VHOG:0000098" - }, { - "val" : "Wikipedia:Endocrine_system" - }, { - "val" : "XAO:0000158" - }, { - "val" : "ZFA:0001158" + "val" : "EHDAA2:0002094" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -19263,126 +21145,52 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000970", - "lbl" : "eye", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organ that detects light.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "light-detecting organ" - }, { - "pred" : "hasRelatedSynonym", - "val" : "visual apparatus", - "xrefs" : [ "EV:0100336" ] + "pred" : "hasExactSynonym", + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { - "val" : "BILA:0000017" - }, { - "val" : "BTO:0000439" - }, { - "val" : "CALOHA:TS-0309" - }, { - "val" : "EFO:0000827" - }, { - "val" : "EV:0100336" - }, { - "val" : "FBbt:00005162" - }, { - "val" : "GAID:69" - }, { - "val" : "MAT:0000140" - }, { - "val" : "MESH:D005123" - }, { - "val" : "MIAA:0000140" + "val" : "CARO:0010000" }, { - "val" : "Wikipedia:Eye" + "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000982", - "lbl" : "skeletal joint", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010199", + "lbl" : "bona-fide anatomical boundary", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].", - "xrefs" : [ "GO_REF:0000034", "VSAO:0000101", "Wikipedia:Joint", "http://dx.plos.org/10.1371/journal.pone.0051070" ] + "val" : "An anatomical boundary that corresponds to some physical discontinuity.", + "xrefs" : [ "CARO:0001004" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "articulation", - "xrefs" : [ "VSAO:0000101" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "joint", - "xrefs" : [ "FMA:7490", "VSAO:0000101" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "articular joint", - "xrefs" : [ "BTO:0001686" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "joints", - "xrefs" : [ "ZFA:0001596" ] - } ], + "comments" : [ "One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. 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however, most visceral muscles in arthropods are actually striated." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "skeleton system" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasNarrowSynonym", - "val" : "set of all bones and joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Skelettsystem", - "xrefs" : [ "BTO:0001486" ] + "val" : "visceral muscle" } ], - "xrefs" : [ { - "val" : "AAO:0000566" - }, { - "val" : "BTO:0001486" - }, { - "val" : "CALOHA:TS-1320" - }, { - "val" : "EFO:0000806" - }, { - "val" : "EHDAA2:0003168" - }, { - "val" : "EMAPA:35773" - }, { - "val" : "FMA:23881" - }, { - "val" : "MA:0000018" - }, { - "val" : "NCIT:C12788" - }, { - "val" : "TAO:0000434" - }, { - "val" : "UMLS:C0037253" - }, { - "val" : "VHOG:0001254" - }, { - "val" : "VSAO:0000027" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" }, { - "val" : "XAO:0003060" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-16T10:17:46Z" }, { - "val" : "ZFA:0000434" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001474", - "lbl" : "bone element", + "id" : "http://purl.obolibrary.org/obo/UBERON_8600006", + "lbl" : "visceral striated muscle tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Skeletal element that is composed of bone tissue.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000057", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/277" ] + "val" : "A striated muscle tissue that is associated with soft internal organs (viscera).", + "xrefs" : [ "PMID:8720463", "https://pressbooks.pub/rbtallitsch/chapter/chapter-6-muscle-tissue/" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "bone organ", - "xrefs" : [ "FMA:5018" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "bone", - "xrefs" : [ "AEO:0000082", "BTO:0000140", "MA:0001459", "VHOG:0001190" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "bones", - "xrefs" : [ "ZFA:0001514" ] + "val" : "striated visceral muscle tissue" } ], - "xrefs" : [ { - "val" : "AAO:0000047" - }, { - "val" : "AEO:0000082" - }, { - "val" : "BTO:0000140" - }, { - "val" : "CALOHA:TS-0088" - }, { - "val" : "EFO:0000298" - }, { - "val" : "EHDAA2:0003082" - }, { - "val" : "EMAPA:32782" + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-6677-8489" }, { - "val" : "ENVO:00002039" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-02-16T10:34:43Z" }, { - "val" : "EV:0100140" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000050", + "lbl" : "part_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a part and its whole" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000050" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { - "val" : "FMA:30317" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "FMA:5018" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "val" : "GAID:92" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "MA:0001459" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "MAT:0000299" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "MIAA:0000299" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { - "val" : "NCIT:C12366" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { - "val" : "SCTID:90780006" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" }, { - "val" : "TAO:0001514" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a core relation that holds between a whole and its part" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { - "val" : "UMLS:C0262950" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "VHOG:0001190" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "val" : "VSAO:0000057" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "Wikipedia:Bone" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "XAO:0000169" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { - "val" : "ZFA:0001514" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "galen:Bone" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "lbl" : "digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A tube extending from the mouth to the anus.", - "xrefs" : [ "Wikipedia:Talk:Human_gastrointestinal_tract", "https://github.com/geneontology/go-ontology/issues/7549" ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "gut" - }, { - "pred" : "hasExactSynonym", - "val" : "digestive tube" - }, { - "pred" : "hasExactSynonym", - "val" : "enteric tract", - "xrefs" : [ "ZFA:0000112" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary canal" - }, { - "pred" : "hasNarrowSynonym", - "val" : "alimentary tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "digestive canal", - "xrefs" : [ "BTO:0000058" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut tube" - } ], + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0010023" - }, { - "val" : "BILA:0000083" - }, { - "val" : "BTO:0000511" - }, { - "val" : "BTO:0000545" - }, { - "val" : "EHDAA2:0000726" - }, { - "val" : "EHDAA:518" - }, { - "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" - }, { - "val" : "FMA:45615" - }, { - "val" : "MA:0000917" - }, { - "val" : "NCIT:C34082" - }, { - "val" : "TAO:0000112" + "val" : "BFO:0000066" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "TGMA:0001819" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" }, { - "val" : "UMLS:C0017189" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" + }, + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "xrefs" : [ { + "val" : "GOREL:0002003" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "VHOG:0000309" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "xrefs" : [ { + "val" : "GOREL:0002004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "WBbt:0005743" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" + }, + "xrefs" : [ { + "val" : "RO:0000053" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." }, { - "val" : "ZFA:0000112" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "galen:AlimentaryTract" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000056" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_41324" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + }, + "xrefs" : [ { + "val" : "RO:0000057" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + }, + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001630", - "lbl" : "muscle organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].", - "xrefs" : [ "GO:0007517" ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "muscle", - "xrefs" : [ "ZFA:0005145" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37474" - }, { - "val" : "EV:0100146" - }, { - "val" : "FMA:5022" - }, { - "val" : "GAID:131" - }, { - "val" : "MA:0000015" - }, { - "val" : "SCTID:71616004" - }, { - "val" : "TAO:0005145" - }, { - "val" : "VHOG:0001245" - }, { - "val" : "XAO:0000172" - }, { - "val" : "ZFA:0005145" - }, { - "val" : "galen:Muscle" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002036", - "lbl" : "striated muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle tissue that contains fibers that are divided by transverse bands into striations.", - "xrefs" : [ "CL:0000737", "GOC:dph", "GOC:mtg_muscle" ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "striated muscle" - } ], - "xrefs" : [ { - "val" : "AAO:0010762" - }, { - "val" : "AEO:0000140" - }, { - "val" : "CALOHA:TS-2047" - }, { - "val" : "EHDAA2:0003140" - }, { - "val" : "EMAPA:36390" - }, { - "val" : "FMA:67905" - }, { - "val" : "MA:0002438" - }, { - "val" : "NCIT:C12436" - }, { - "val" : "UMLS:C1331262" - }, { - "val" : "WBbt:0005779" - }, { - "val" : "Wikipedia:Striated_muscle" - }, { - "val" : "galen:StriatedMuscle" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002050", - "lbl" : "embryonic structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that is part of an embryo.", - "xrefs" : [ "BTO:0000174", "ZFIN:curator" ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "developing embryonic structure", - "xrefs" : [ "FBbt:00004208" ] - }, { - "pred" : "hasExactSynonym", - "val" : "embryonic anatomical structure", - "xrefs" : [ "RETIRED_EHDAA2:0003169" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonale Struktur", - "xrefs" : [ "BTO:0000174" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "embryonic structures", - "xrefs" : [ "ZFA:0001105" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000138" - }, { - "val" : "BILA:0000034" - }, { - "val" : "BTO:0000174" - }, { - "val" : "CALOHA:TS-2110" - }, { - "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" - }, { - "val" : "FMA:69067" - }, { - "val" : "GAID:407" - }, { - "val" : "MESH:D004628" - }, { - "val" : "NCIT:C13229" - }, { - "val" : "RETIRED_EHDAA2:0003169" - }, { - "val" : "SCTID:667009" - }, { - "val" : "TAO:0001105" - }, { - "val" : "UMLS:C0013948" - }, { - "val" : "VSAO:0000178" + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { - "val" : "XAO:0003042" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "ZFA:0001105" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", - "lbl" : "trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. 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" }, - "comments" : [ "Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "NC", - "xrefs" : [ "XAO:0000048" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "crista neuralis", - "xrefs" : [ "Wikipedia:Neural_crest" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neural crest material", - "xrefs" : [ "VHOG:0000057" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010578" - }, { - "val" : "BTO:0001764" - }, { - "val" : "CALOHA:TS-0676" - }, { - "val" : "EHDAA2:0004419" - }, { - "val" : "EMAPA:32737" - }, { - "val" : "FMA:86666" - }, { - "val" : "GAID:1310" - }, { - "val" : "MAT:0000066" - }, { - "val" : "MESH:D009432" - }, { - "val" : "MIAA:0000066" - }, { - "val" : "NCIT:C34222" - }, { - "val" : "SCTID:361462002" - }, { - "val" : "UMLS:C0027789" - }, { - "val" : "VHOG:0000057" - }, { - "val" : "Wikipedia:Neural_crest" - }, { - "val" : "XAO:0000048" - }, { - "val" : "ZFA:0000045" - }, { - "val" : "neuronames:1366" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002346", - "lbl" : "neurectoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002113", + "lbl" : "has presynaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Embryonic ectoderm that gives rise to nervous tissue.", - "xrefs" : [ "Wikipedia:Neuroectoderm" ] + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neural ectoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "neuroectoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epithelium tubi neuralis; neuroectoderma", - "xrefs" : [ "Wikipedia:Neuroectoderm" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neuaral ectoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral neurogenic region", - "xrefs" : [ "VHOG:0000150" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011074" - }, { - "val" : "BILA:0000039" - }, { - "val" : "CALOHA:TS-1212" - }, { - "val" : "EHDAA2:0001248" - }, { - "val" : "EHDAA:1498" - }, { - "val" : "EHDAA:255" - }, { - "val" : "EMAPA:16073" - }, { - "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" - }, { - "val" : "FMA:87657" - }, { - "val" : "MAT:0000176" - }, { - "val" : "MIAA:0000176" - }, { - "val" : "NCIT:C34228" - }, { - "val" : "TAO:0001120" - }, { - "val" : "UMLS:C1518271" - }, { - "val" : "VHOG:0000150" - }, { - "val" : "Wikipedia:Neuroectoderm" - }, { - "val" : "XAO:0000042" - }, { - "val" : "ZFA:0001120" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002365", - "lbl" : "exocrine gland", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas.", - "xrefs" : [ "Wikipedia:Exocrine_gland" ] + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ducted gland", - "xrefs" : [ "AEO:0000097" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "glandula exocrina", - "xrefs" : [ "Wikipedia:Exocrine_gland" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000097" - }, { - "val" : "BTO:0000765" - }, { - "val" : "CALOHA:TS-2012" - }, { - "val" : "EHDAA2:0003097" - }, { - "val" : "EMAPA:35327" - }, { - "val" : "FMA:9596" - }, { - "val" : "GAID:34" - }, { - "val" : "MA:0002564" - }, { - "val" : "MESH:D005088" - }, { - "val" : "NCIT:C12712" - }, { - "val" : "SCTID:115976003" - }, { - "val" : "UMLS:C0015282" - }, { - "val" : "Wikipedia:Exocrine_gland" - } ], + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002368", - "lbl" : "endocrine gland", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].", - "xrefs" : [ "Wikipedia:Endocrine_gland" ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - 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See also: Leydig and epigonal organs" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider placement of NCIT:C53466 medullary bone" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "lbl" : "connective tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of connective tissue", - "xrefs" : [ "FMA:9640" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus connectivus" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bindegewebe", - "xrefs" : [ "BTO:0000421" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000098" - }, { - "val" : "BTO:0000421" - }, { - "val" : "CALOHA:TS-2009" - }, { - "val" : "EFO:0000952" - }, { - "val" : "EMAPA:35251" - }, { - "val" : "FMA:9640" - }, { - "val" : "GAID:100" - }, { - "val" : "MA:0000011" - }, { - "val" : "MAT:0000301" - }, { - "val" : "MESH:D003238" - }, { - "val" : "MIAA:0000301" - }, { - "val" : "NCIT:C12374" - }, { - "val" : "SCTID:361919005" - }, { - "val" : "TAO:0001641" - }, { - "val" : "UMLS:C0009780" - }, { - "val" : "VSAO:0000017" - }, { - "val" : "XAO:0001017" - }, { - "val" : "ZFA:0001632" - }, { - "val" : "galen:ConnectiveTissue" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "lbl" : "muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", - "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." }, - "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] - }, { - "pred" : "hasExactSynonym", - "val" : "textus muscularis" - } ], - "xrefs" : [ { - "val" : "AAO:0000306" - }, { - "val" : "AEO:0000122" - }, { - "val" : "CALOHA:TS-0642" - }, { - "val" : "EHDAA2:0003122" - }, { - "val" : "EMAPA:32715" - }, { - "val" : "FMA:9641" - }, { - "val" : "MA:0002437" - }, { - "val" : "MESH:D009132" - }, { - "val" : "NCIT:C12435" - }, { - "val" : "SCTID:91727004" - }, { - "val" : "UMLS:C2328219" - }, { - "val" : "Wikipedia:Muscle_tissue" - }, { - "val" : "galen:MuscleTissue" - } ], + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "haematological system" - }, { - "pred" : "hasExactSynonym", - "val" : "haemopoietic system" - }, { - "pred" : "hasExactSynonym", - "val" : "organa haemopoietica" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Blutbildungssystem", - "xrefs" : [ "BTO:0000570" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "haematopoietic system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematological system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hematolymphoid system" - }, { - "pred" : "hasRelatedSynonym", - "val" : "hemopoietic system" - } ], - "xrefs" : [ { - "val" : "AAO:0011002" - }, { - "val" : "BTO:0000570" - }, { - "val" : "CALOHA:TS-0449" - }, { - "val" : "EFO:0000798" - }, { - "val" : "EMAPA:35402" - }, { - "val" : "EV:0100045" - }, { - "val" : "FMA:9667" - }, { - "val" : "GAID:1008" - }, { - "val" : "MA:0002434" - }, { - "val" : "MAT:0000022" - }, { - "val" : "MESH:D006413" - }, { - "val" : "MIAA:0000022" - }, { - "val" : "NCIT:C12909" - }, { - "val" : "SCTID:362587009" - }, { - "val" : "TAO:0005023" - }, { - "val" : "UMLS:C0018957" - }, { - "val" : "VHOG:0001624" - }, { - "val" : "Wikipedia:Haematopoiesis" + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. 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" }, { - "val" : "XAO:0000122" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { - "val" : "ZFA:0005023" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002405", - "lbl" : "immune system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies.", - "xrefs" : [ "Wikipedia:Immune_system" ] + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "xrefs" : [ { - "val" : "AAO:0011003" - }, { - "val" : "BILA:0000104" - }, { - "val" : "BTO:0005810" - }, { - "val" : "FMA:9825" - }, { - "val" : "GAID:328" - }, { - "val" : "MA:0002711" - }, { - "val" : "MESH:D007107" - }, { - "val" : "NCIT:C12735" - }, { - "val" : "SCTID:362590003" - }, { - "val" : "TAO:0001159" - }, { - "val" : "UMLS:C0020962" - }, { - "val" : "VHOG:0001247" - }, { - "val" : "Wikipedia:Immune_system" - }, { - "val" : "XAO:0003152" - }, { - "val" : "ZFA:0001159" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "lbl" : "bone tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). 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For example, in the realm of anatomy this should hold between an artery and an anatomical structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002530", - "lbl" : "gland", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that functions as a secretory or excretory organ.", - "xrefs" : [ "MGI:csmith", "MP:0002163" ] + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "glandular organ", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Druese", - "xrefs" : [ "BTO:0000522" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "glandula", - "xrefs" : [ "BTO:0000522", "Wikipedia:Gland" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000212" - }, { - "val" : "AEO:0000096" - }, { - "val" : "BTO:0000522" - }, { - "val" : "EFO:0000797" - }, { - "val" : "EHDAA2:0003096" - }, { - "val" : "EHDAA:2161" - }, { - "val" : "EMAPA:18425" - }, { - "val" : "FBbt:00100317" - }, { - "val" : "FMA:7146" - }, { - "val" : "FMA:86294" - }, { - "val" : "HAO:0000375" - }, { - "val" : "MA:0003038" - }, { - "val" : "MAT:0000021" - }, { - "val" : "MIAA:0000021" - }, { - "val" : "NCIT:C13319" - }, { - "val" : "SCTID:134358001" - }, { - "val" : "UMLS:C1285092" - }, { - "val" : "Wikipedia:Gland" - }, { - "val" : "WikipediaCategory:Glands" - }, { - "val" : "galen:Gland" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. 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In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" + }, + "comments" : [ "This is the transitive form of the develops from relation" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] + "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" - } ], - "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" - }, { - "val" : "NCIT:C34007" - }, { - "val" : "galen:Cavity" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segmental plate" - }, { - "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] - } ], + "val" : "has developmental precursor" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "inverse of directly develops from" + }, + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" - }, { - "val" : "XAO:0000057" - }, { - "val" : "ZFA:0000279" + "val" : "RO:0002211" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].", - "xrefs" : [ "Wikipedia:Blood_island_of_umbilical_vesicle" ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ventral lateral plate mesoderm" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "blood islands" - }, { - "pred" : "hasRelatedSynonym", - "val" : "VBI" - }, { - "pred" : "hasRelatedSynonym", - "val" : "caudal hematopoietic tissue" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior ICM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "posterior blood island" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ventral blood island" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011006" - }, { - "val" : "EFO:0003489" - }, { - "val" : "EHDAA:207" - }, { - "val" : "NCIT:C34113" - }, { - "val" : "TAO:0000094" - }, { - "val" : "TE:E5.11.2.0.0.0.4" - }, { - "val" : "UMLS:C1511224" - }, { - "val" : "VHOG:0000085" - }, { - "val" : "Wikipedia:Blood_island_of_umbilical_vesicle" - }, { - "val" : "XAO:0000067" - }, { - "val" : "ZFA:0000094" + "val" : "RO:0002212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "lbl" : "axial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.", - "xrefs" : [ "GO:0048318", "Wikipedia:Chordamesoderm" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "chordamesoderm", - "xrefs" : [ "Wikipedia:Chordamesoderm" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011017" - }, { - "val" : "EFO:0003647" - }, { - "val" : "TAO:0001204" - }, { - "val" : "VHOG:0000107" - }, { - "val" : "Wikipedia:Chordamesoderm" - }, { - "val" : "XAO:0000205" - }, { - "val" : "ZFA:0001204" + "val" : "RO:0002213" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "lbl" : "neural plate", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].", - "xrefs" : [ "ISBN:0815318960", "OMD:neural+plate", "Wikipedia:Neural_plate", "ZFIN:curator" ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "lamina neuralis", - "xrefs" : [ "Wikipedia:Neural_plate" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011072" - }, { - "val" : "BTO:0001765" - }, { - "val" : "DHBA:10153" - }, { - "val" : "DMBA:15565" - }, { - "val" : "EHDAA:346" - }, { - "val" : "EHDAA:902" - }, { - "val" : "EMAPA:35593" - }, { - "val" : "FMA:293879" - }, { - "val" : "NCIT:C34225" - }, { - "val" : "RETIRED_EHDAA2:0001252" - }, { - "val" : "TAO:0000132" - }, { - "val" : "UMLS:C0920623" - }, { - "val" : "VHOG:0000068" - }, { - "val" : "Wikipedia:Neural_plate" - }, { - "val" : "XAO:0000249" - }, { - "val" : "ZFA:0000132" - }, { - "val" : "neuronames:1362" + "val" : "RO:0002215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "lbl" : "paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002216", + "lbl" : "capable of part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].", - "xrefs" : [ "GO:0048339", "https://github.com/obophenotype/uberon/issues/30" ] + "val" : "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "paraxial mesenchyme", - "xrefs" : [ "ZFA:0000255", "https://github.com/obophenotype/uberon/issues/30", "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "somitic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesoderma paraxiale", - "xrefs" : [ "Wikipedia:Paraxial_mesoderm" ] - } ], "xrefs" : [ { - "val" : "AAO:0010568" - }, { - "val" : "EFO:0003515" - }, { - "val" : "EMAPA:16183" - }, { - "val" : "EMAPA:16751" - }, { - "val" : "FMA:293145" - }, { - "val" : "NCIT:C34244" - }, { - "val" : "SCTID:361475002" - }, { - "val" : "TAO:0000255" - }, { - "val" : "UMLS:C1284009" - }, { - "val" : "VHOG:0000114" - }, { - "val" : "Wikipedia:Paraxial_mesoderm" - }, { - "val" : "XAO:0000259" - }, { - "val" : "ZFA:0000255" + "val" : "RO:0002216" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "capable_of_part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "lbl" : "lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002219", + "lbl" : "surrounded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].", - "xrefs" : [ "MP:0010117", "Wikipedia:Lateral_plate_mesoderm" ] + "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002220", + "lbl" : "adjacent to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x adjacent to y if and only if x and y share a boundary." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "LPM", - "xrefs" : [ "ZFA:0000121" ] - }, { - "pred" : "hasExactSynonym", - "val" : "lateral mesoderm", - "xrefs" : [ "GO:0048368" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "lateral plate" - }, { - "pred" : "hasRelatedSynonym", - "val" : "lateral plate mesenchyme", - "xrefs" : [ "EHDAA2:0000919" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesoderma laminae lateralis", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0010574" - }, { - "val" : "EHDAA2:0000919" - }, { - "val" : "EHDAA:379" - }, { - "val" : "EMAPA:16179" - }, { - "val" : "FMA:293149" - }, { - "val" : "NCIT:C34199" - }, { - "val" : "SCTID:361477005" - }, { - "val" : "TAO:0000121" - }, { - "val" : "UMLS:C1517749" - }, { - "val" : "VHOG:0000118" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm" - }, { - "val" : "XAO:0000311" - }, { - "val" : "ZFA:0000121" + "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0006258" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation acts as a join point with BSPO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "adjacent_to" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003082", - "lbl" : "myotome", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002221", + "lbl" : "surrounds", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.", - "xrefs" : [ "AEO:0001018" ] + "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - 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Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0010015" - }, { - "val" : "AEO:0000024" - }, { - "val" : "BILA:0000024" - }, { - "val" : "CARO:0000024" - }, { - "val" : "EHDAA2:0003024" - }, { - "val" : "HAO:0000024" - }, { - "val" : "TADS:0000598" - }, { - "val" : "TAO:0000496" - }, { - "val" : "TGMA:0001837" - }, { - "val" : "VHOG:0001723" - }, { - "val" : "XAO:0003041" - }, { - "val" : "ZFA:0000496" + "val" : "RO:0002230" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "ends_with" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "lbl" : "mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002231", + "lbl" : "has start location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. 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TODO - add spatial relationships to halves of LPM. 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It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "false" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002263", + "lbl" : "acts upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - 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"val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" + "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004290", - "lbl" : "dermomyotome", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002264", + "lbl" : "acts upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The bilaminar epithelium formed from the myotome and dermatome.", - "xrefs" : [ "AEO:0000214" ] + "val" : "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "dermamyotome", - "xrefs" : [ "VHOG:0000676" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "dermomyotomes", - "xrefs" : [ "VHOG:0000676" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010572" - }, { - "val" : "AEO:0000214" - }, { - "val" : "EHDAA2:0003259" - }, { - "val" : "EMAPA:31109" - }, { - "val" : "FMA:295654" - }, { - "val" : "NCIT:C34140" - }, { - "val" : "TAO:0001513" - }, { - "val" : "UMLS:C1511786" - }, { - "val" : "VHOG:0000676" - }, { - "val" : "ZFA:0001513" + "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004456", - "lbl" : "entire sense organ system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002285", + "lbl" : "developmentally replaces", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Sum of all sensory systems in an organism.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "sense organ system", - "xrefs" : [ "FMA:78499" ] - } ], - "xrefs" : [ { - "val" : "FMA:78499" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004716", - "lbl" : "conceptus", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002286", + "lbl" : "developmentally succeeded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].", - "xrefs" : [ "BTO:0003834", "Wikipedia:Conceptus" ] + "val" : "Inverse of developmentally preceded by" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002287", + "lbl" : "part of developmental precursor of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002292", + "lbl" : "expresses", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002295", + "lbl" : "results in developmental progression of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "embryo plus adnexa" - } ], "xrefs" : [ { - "val" : "AEO:0000194" - }, { - "val" : "BTO:0003834" - }, { - "val" : "EHDAA2:0000001" - }, { - "val" : "EHDAA2:0003235" - }, { - "val" : "EMAPA:36040" - }, { - "val" : "NCIT:C34131" - }, { - "val" : "UMLS:C1516779" - }, { - "val" : "Wikipedia:Conceptus" + "val" : "RO:0002295" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" + "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_developmental_progression_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://wiki.geneontology.org/index.php/Ontology_extensions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004734", - "lbl" : "gastrula", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002296", + "lbl" : "results in development of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the gastrula stage.", - "xrefs" : [ "Wikipedia:Gastrula", "Wikipedia:Trilaminar_blastocyst" ] + "val" : "p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "gastrula embryo", - "xrefs" : [ "BILA:0000060" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocystis trilaminaris", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "tri-laminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastocyst", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar blastoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disc", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar disk", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trilaminar germ", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BILA:0000060" - }, { - "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" - }, { - "val" : "FMA:293108" - }, { - "val" : "GAID:1302" - }, { - "val" : "MESH:D005775" - }, { - "val" : "MIAA:0000179" - }, { - "val" : "NCIT:C34057" - }, { - "val" : "NCIT:C34058" - }, { - "val" : "UMLS:C0017199" - }, { - "val" : "UMLS:C1284022" - }, { - "val" : "Wikipedia:Gastrula" - }, { - "val" : "Wikipedia:Trilaminar_blastocyst" + "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007012" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_development_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004755", - "lbl" : "skeletal tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002297", + "lbl" : "results in formation of anatomical entity", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].", - "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000015", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/134" ] - }, - "comments" : [ "Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:37744" - }, { - "val" : "MA:0003047" - }, { - "val" : "SCTID:309311006" - }, { - "val" : "VSAO:0000015" - }, { - "val" : "XAO:0004038" - }, { - "val" : "ZFA:0005619" + "val" : "RO:0002297" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_formation_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004765", - "lbl" : "skeletal element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002298", + "lbl" : "results in morphogenesis of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" - }, { - "val" : "galen:SkeletalStructure" + "val" : "RO:0002298" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_morphogenesis_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002299", + "lbl" : "results in maturation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] + "val" : "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" - }, { - "val" : "MA:0003007" - }, { - "val" : "SCTID:361827000" - }, { - "val" : "VSAO:0000181" + "val" : "RO:0002299" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_maturation_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002304", + "lbl" : "causally upstream of, positive effect", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], + "comments" : [ "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - 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"subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "FBbt:00005811" + "val" : "RO:0002305" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002411" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of,_negative_effect" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - 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If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "presumptive epidermis", - "xrefs" : [ "ZFA:0001376" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000470" - }, { - "val" : "EFO:0003466" - }, { - "val" : "TAO:0001376" - }, { - "val" : "XAO:0004132" - }, { - "val" : "ZFA:0001376" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://dbpedia.org/ontology/drainsTo" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://en.wikipedia.org/wiki/Tributary" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "lbl" : "presumptive mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002379", + "lbl" : "spatially coextensive with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Presumptive structure of the blastula that will develop into mesoderm.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002380", + "lbl" : "branching part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "xrefs" : [ { - "val" : "AAO:0000476" - }, { - "val" : "EFO:0003467" - }, { - "val" : "TAO:0001377" - }, { - "val" : "ZFA:0001377" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2212" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85994" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0006984", - "lbl" : "anatomical surface", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002384", + "lbl" : "has developmental potential involving", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002385", + "lbl" : "has potential to developmentally contribute to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002386", + "lbl" : "has potential to developmentally induce", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002387", + "lbl" : "has potential to develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002388", + "lbl" : "has potential to directly develop into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002404", + "lbl" : "causally downstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", - "xrefs" : [ "CARO:0001002" ] + "val" : "inverse of upstream of" }, - "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "BILA:0000010" - }, { - "val" : "CARO:0001002" - }, { - "val" : "EHDAA2_RETIRED:0003192" - }, { - "val" : "FMA:24137" - }, { - "val" : "NCIT:C34022" - }, { - "val" : "UMLS:C1515977" + "val" : "RO:0002404" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", - "lbl" : "cleaving embryo", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Organism at the cleavage stage.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "xrefs" : [ { - "val" : "BILA:0000058" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", - "lbl" : "presumptive gut", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future digestive tract" - }, { - "pred" : "hasExactSynonym", - "val" : "future digestive tube" - }, { - "pred" : "hasExactSynonym", - "val" : "future gut" - }, { - "pred" : "hasExactSynonym", - "val" : "primitive gut" - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic digestive tube" - }, { - "pred" : "hasRelatedSynonym", - "val" : "primordial digestive tube" - }, { - "pred" : "hasRelatedSynonym", - "val" : "primordial gut" - } ], + "definition" : { + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BILA:0000084" - }, { - "val" : "NCIT:C34268" - }, { - "val" : "SCTID:360394002" - }, { - "val" : "UMLS:C1514442" + "val" : "RO:0002411" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007100", - "lbl" : "primary circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].", - "xrefs" : [ "GO:0007507" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "comments" : [ "Gene notes: Bmp, Nkx, Gata" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "dorsal tube", - "xrefs" : [ "Wikipedia:Heart" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "heart", - "xrefs" : [ "GO:0007507" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "adult heart", - "xrefs" : [ "FBbt:00003154" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "TADS:0000147" - }, { - "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007135", - "lbl" : "neural keel", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; 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Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "prospective neuroectoderm", - "xrefs" : [ "ZFA:0000063" ] - }, { - "pred" : "hasExactSynonym", - "val" : "prospective vegetal ectoderm", - "xrefs" : [ "ZFA:0000063" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003424" - }, { - "val" : "TAO:0000063" - }, { - "val" : "ZFA:0000063" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007285", - "lbl" : "presumptive paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. 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Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. 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Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. 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Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. 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Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. 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See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "definition" : { + "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "add to RO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034769", - "lbl" : "lymphomyeloid tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", + "lbl" : "layer part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "FMA:79770" - }, { - "val" : "NCIT:C41168" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", + "lbl" : "posteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] + "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], - "xrefs" : [ { - "val" : "CARO:0020001" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", + "lbl" : "protects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", + "lbl" : "proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034969", - "lbl" : "epithelial layer of duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", + "lbl" : "sexually_homologous_to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "duct epithelium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ductal epithelium" - } ], - "xrefs" : [ { - "val" : "NCIT:C25787" - }, { - "val" : "UMLS:C1512086" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", + "lbl" : "site_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], - "xrefs" : [ { - "val" : "FMA:293105" + "pred" : "hasRelatedSynonym", + "val" : "capable_of_has_part" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24822,411 +25530,916 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", - "lbl" : "visceral muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", + "lbl" : "subdivision of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] - }, - "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral muscle" - } ], + "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:17:46Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600006", - "lbl" : "visceral striated muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A striated muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "PMID:8720463", "https://pressbooks.pub/rbtallitsch/chapter/chapter-6-muscle-tissue/" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "striated visceral muscle tissue" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:34:43Z" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", - "lbl" : "blood_and_immune_upper_slim", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", + "lbl" : "transitively distally connected to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-03-31T09:17:34Z" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", - "lbl" : "eye_upper_slim", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", + "lbl" : "transitively proximally connected to", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "comments" : [ "a subset of general classes related to specific cell types in the eye." ] + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", - "lbl" : "general_cell_types_upper_slim", + "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", + "lbl" : "trunk_part_of", "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "comments" : [ "a subset of general classes of cell types in the cell ontology." ] + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", - "lbl" : "kidney_upper_slim", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { - "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], + "definition" : { + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." + }, "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-11-22T11:18:57Z" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", - "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", - "lbl" : "latin term", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } + } }, { - "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", - "lbl" : "plural term", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" + } ] + } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", - "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], + "xrefs" : [ { + "val" : "IAO:0000233" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "definition" : { + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, + "xrefs" : [ { + "val" : "IAO:0000700" + } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" + }, { + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." + "val" : "A synonym type for describing abbreviations or initalisms" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "A synonym type for describing pluralization synonyms" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "definition" : { + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/RO_0002259", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", + "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], + "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-03-31T09:17:34Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", + "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", + "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", + "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { + "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + "pred" : "http://purl.org/dc/terms/date", + "val" : "2023-11-22T11:18:57Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", + "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", + "lbl" : "latin term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", + "lbl" : "plural term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", + "lbl" : "a mis-spelling that is in common use and thus recorded", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -25242,11 +26455,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -25263,6 +26478,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -25278,11 +26494,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -25298,23 +26516,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -25324,6 +26571,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -27117,6 +28376,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0001667", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0016477" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001677", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0022618" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001677", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006413" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0001677", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_0044207" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0001704", "pred" : "is_a", @@ -27523,6 +28794,58 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006310", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0006259" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009059" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0019538" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0010467" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0006414" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/RO_0002224", + "obj" : "http://purl.obolibrary.org/obo/GO_0006413" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006412", + "pred" : "http://purl.obolibrary.org/obo/RO_0002230", + "obj" : "http://purl.obolibrary.org/obo/GO_0006415" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006413", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044237" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006413", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006413", + "pred" : "http://purl.obolibrary.org/obo/RO_0002224", + "obj" : "http://purl.obolibrary.org/obo/GO_0001677" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006414", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009059" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006414", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006415", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032984" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006415", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006810", "pred" : "is_a", @@ -27735,10 +29058,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009059", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044249" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0009059", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_1901576" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0009314", "pred" : "is_a", @@ -27967,6 +29286,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0019226", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0007268" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0019538", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044238" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0019538", + "pred" : "http://purl.obolibrary.org/obo/RO_0004007", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0019724", "pred" : "is_a", @@ -28003,6 +29330,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0021915", "pred" : "http://purl.obolibrary.org/obo/RO_0002296", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022411", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022411", + "pred" : "http://purl.obolibrary.org/obo/RO_0002590", + "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0022414", "pred" : "is_a", @@ -28015,6 +29350,38 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0022600", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0007586" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022607", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022607", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0044085" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022607", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_0005575" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022613", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0044085" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0065003" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0071826" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0022613" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0022618", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_1990904" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0023052", "pred" : "is_a", @@ -28247,6 +29614,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0032940", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0140352" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0032984", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0022411" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0032984", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0043933" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0032984", + "pred" : "http://purl.obolibrary.org/obo/RO_0002590", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", "pred" : "is_a", @@ -28483,6 +29862,26 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0043292", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0043933", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0043933", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044085", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0071840" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044207", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_1990904" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044207", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0005737" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044237", "pred" : "is_a", @@ -28491,6 +29890,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044237", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0044238", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0008152" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0044249", "pred" : "is_a", @@ -28947,6 +30350,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0062023", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0065003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0022607" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0065003", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0043933" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0065003", + "pred" : "http://purl.obolibrary.org/obo/RO_0002588", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0065007", "pred" : "is_a", @@ -28972,9 +30387,13 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099503" }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0071704", + "sub" : "http://purl.obolibrary.org/obo/GO_0071826", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0008152" + "obj" : "http://purl.obolibrary.org/obo/GO_0043933" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0071826", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_1990904" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0071840", "pred" : "is_a", @@ -29259,14 +30678,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140546", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0098542" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1902105", "pred" : "is_a", @@ -29299,6 +30710,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_1903706", "pred" : "http://purl.obolibrary.org/obo/RO_0002211", "obj" : "http://purl.obolibrary.org/obo/GO_0030097" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_1990904", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0032991" }, { "sub" : "http://purl.obolibrary.org/obo/GO_2000026", "pred" : "is_a", @@ -29611,6 +31026,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070046", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0070045" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -29839,6 +31266,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000050216", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000001006" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000020", "pred" : "is_a", @@ -33752,6 +35183,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000006", @@ -34666,6 +36101,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002371" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001677", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0044207" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001704", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], @@ -34897,6 +36339,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000034" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019538", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008152" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0004007", + "fillerId" : "http://purl.obolibrary.org/obo/PR_000000001" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0019724", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0002376" ], @@ -34911,6 +36360,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001049" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022411", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005575" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022600", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0003008" ], @@ -34918,6 +36374,20 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007586" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022607", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005575" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0022618", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_1990904" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0023061", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0032940" ], @@ -35023,6 +36493,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032984", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022411" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035148", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], @@ -35093,6 +36570,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043933", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045321", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0001775" ], @@ -35303,6 +36787,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0065003", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0070013", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031974" ], @@ -35317,6 +36808,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0099500" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0071826", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_1990904" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0072175", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0035148" ], @@ -36115,6 +37613,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/subsets/general_cell_types_upper_slim.obo b/subsets/general_cell_types_upper_slim.obo index ff7dddd78..ce6d8abd7 100644 --- a/subsets/general_cell_types_upper_slim.obo +++ b/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -121,7 +126,7 @@ name: neuronal receptor cell def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] subset: cellxgene_subset synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000101 ! sensory neuron is_a: CL:0000197 ! sensory receptor cell intersection_of: CL:0000197 ! sensory receptor cell @@ -132,7 +137,7 @@ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in senso id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] @@ -146,7 +151,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -171,7 +176,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -213,7 +218,7 @@ def: "A cell that is within the developmental lineage of gametes and is able to comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim subset: ubprop:upper_level -xref: ZFA:0009016 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: capable_of GO:0022414 ! reproductive process @@ -228,7 +233,7 @@ synonym: "colony forming unit monocyte" RELATED [] synonym: "monocyte stem cell" RELATED [] xref: CALOHA:TS-1195 xref: FMA:83553 -xref: ZFA:0009017 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -252,7 +257,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -275,7 +280,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell @@ -297,7 +302,7 @@ synonym: "early lymphocyte progenitor" RELATED [] synonym: "ELP" RELATED OMO:0003000 [] synonym: "lymphoid stem cell" RELATED [] synonym: "lymphopoietic stem cell" RELATED [] -xref: ZFA:0009023 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009023 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell @@ -312,7 +317,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -332,10 +337,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -351,7 +356,7 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -367,14 +372,14 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -383,7 +388,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -395,7 +400,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -418,7 +423,7 @@ xref: CALOHA:TS-1001 xref: FMA:62870 xref: MESH:D013601 xref: VHOG:0001479 -xref: ZFA:0009046 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009046 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000542 {is_inferred="true"} ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity @@ -438,7 +443,7 @@ xref: BTO:0000968 xref: CALOHA:TS-0721 xref: FMA:66781 xref: MESH:D010010 -xref: ZFA:0009047 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell @@ -475,7 +480,7 @@ xref: BTO:0000539 xref: BTO:0001026 xref: CALOHA:TS-0422 xref: FMA:62854 -xref: ZFA:0009048 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte intersection_of: CL:0000766 ! myeloid leukocyte @@ -513,10 +518,10 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "motoneuron" EXACT [] xref: BTO:0000312 -xref: FBbt:00005123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83617 xref: WBbt:0005409 -xref: ZFA:0009052 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000527 ! efferent neuron property_value: RO:0002175 NCBITaxon:9606 @@ -526,11 +531,11 @@ name: sensory neuron def: "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." [ISBN:0721662544] subset: human_reference_atlas xref: BTO:0001037 -xref: FBbt:00005124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:84649 xref: MESH:D011984 xref: WBbt:0005759 -xref: ZFA:0009053 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009053 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000526 ! afferent neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception @@ -544,7 +549,7 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 -xref: ZFA:0009064 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) @@ -563,9 +568,9 @@ synonym: "neuroglia" RELATED [] synonym: "neuroglial cell" EXACT [] xref: BTO:0002606 xref: CALOHA:TS-0415 -xref: FBbt:00005144 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 -xref: ZFA:0009073 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 @@ -574,7 +579,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -598,7 +603,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -615,7 +620,7 @@ synonym: "fat cell" EXACT [] xref: BTO:0000443 xref: CALOHA:TS-0012 xref: FMA:63880 -xref: ZFA:0009082 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009082 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell @@ -629,7 +634,7 @@ comment: Note change of name; nearly all somatic cells can present antigens to T subset: blood_and_immune_upper_slim subset: cellxgene_subset synonym: "APC" RELATED OMO:0003000 [] -xref: ZFA:0009088 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009088 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: capable_of GO:0002504 ! antigen processing and presentation of peptide or polysaccharide antigen via MHC class II @@ -642,7 +647,7 @@ def: "A pigment cell is a cell that contains pigment granules." [GOC:tfm] synonym: "chromatocyte" EXACT [] synonym: "chromatophore" EXACT [] xref: VHOG:0001678 -xref: ZFA:0009090 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009090 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000325 ! stuff accumulating cell [Term] @@ -658,7 +663,7 @@ xref: CALOHA:TS-0613 xref: FMA:70545 xref: MESH:D008544 xref: VHOG:0001679 -xref: ZFA:0009091 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome @@ -691,7 +696,7 @@ name: exocrine cell def: "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." [ISBN:0198547684] subset: general_cell_types_upper_slim xref: FMA:16014 -xref: ZFA:0009092 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland @@ -706,7 +711,7 @@ subset: general_cell_types_upper_slim subset: human_reference_atlas synonym: "endocrinocyte" EXACT [] xref: FMA:83809 -xref: ZFA:0009096 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0000949 ! endocrine system property_value: RO:0002175 NCBITaxon:9606 @@ -728,14 +733,14 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000188 @@ -748,7 +753,7 @@ synonym: "skeletal muscle cell" EXACT [] xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 -xref: ZFA:0009115 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue @@ -769,7 +774,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -795,27 +800,27 @@ def: "A cell specialized to detect and transduce light." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 -xref: FBbt:00004211 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 -xref: ZFA:0009127 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -827,7 +832,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -839,7 +844,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -849,7 +854,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -884,7 +889,7 @@ subset: cellxgene_subset xref: BTO:0001044 xref: FMA:83806 xref: MESH:D010586 -xref: ZFA:0009140 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009140 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0000473 ! defensive cell @@ -907,7 +912,7 @@ xref: CALOHA:TS-0587 xref: FMA:63261 xref: FMA:83585 xref: MESH:D008264 -xref: ZFA:0009141 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009141 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte @@ -935,7 +940,7 @@ xref: CALOHA:TS-0068 xref: FMA:62869 xref: MESH:D001402 xref: VHOG:0001480 -xref: ZFA:0009142 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009142 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity @@ -963,7 +968,7 @@ is_a: CL:0000000 ! cell [Term] id: CL:0000327 name: extracellular matrix secreting cell -xref: ZFA:0009162 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000499 ! stromal cell [Term] @@ -971,7 +976,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -982,7 +987,7 @@ id: CL:0000349 name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] subset: general_cell_types_upper_slim -xref: ZFA:0009176 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure @@ -1000,7 +1005,7 @@ name: multi-potent skeletal muscle stem cell def: "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." [PMID:18282570] comment: Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. xref: FMA:86767 -xref: ZFA:0009179 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009179 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell is_a: CL:0000188 ! cell of skeletal muscle intersection_of: CL:0000048 ! multi fate stem cell @@ -1025,14 +1030,14 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -1048,7 +1053,7 @@ xref: BTO:0002042 xref: CALOHA:TS-0194 xref: FMA:83036 xref: MESH:D003713 -xref: ZFA:0009209 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell intersection_of: CL:0000738 ! leukocyte @@ -1089,7 +1094,7 @@ subset: general_cell_types_upper_slim subset: human_reference_atlas xref: BTO:0002064 xref: FMA:83624 -xref: ZFA:0009226 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009226 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -1102,7 +1107,7 @@ subset: cellxgene_subset synonym: "cardiac muscle progenitor cell" EXACT [] synonym: "cardiomyocyte progenitor cell" EXACT [] xref: FMA:84797 -xref: ZFA:0009234 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009234 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast intersection_of: CL:0000056 ! myoblast @@ -1118,7 +1123,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -1130,7 +1135,7 @@ name: skeletal muscle myoblast def: "A myoblast that differentiates into skeletal muscle fibers." [SANBI:mhl] synonym: "skeletal myoblast" EXACT [] xref: FMA:84799 -xref: ZFA:0009236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000056 ! myoblast @@ -1153,7 +1158,7 @@ def: "A neuron which conveys sensory information centrally from the periphery." subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 -xref: ZFA:0009238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron property_value: RO:0002175 NCBITaxon:9606 @@ -1162,7 +1167,7 @@ id: CL:0000527 name: efferent neuron def: "A neuron which sends impulses peripherally to activate muscles or secretory cells." [MESH:D009476] synonym: "output neuron" EXACT [] -xref: ZFA:0009239 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000540 ! neuron [Term] @@ -1176,16 +1181,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1195,7 +1200,7 @@ def: "A cell that originates from the neural crest and differentiates into a pig comment: Derived from UBERON:0002342 neural crest. xref: BTO:0003217 xref: FMA:83377 -xref: ZFA:0009249 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009249 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell @@ -1212,7 +1217,7 @@ xref: CALOHA:TS-0583 xref: FMA:62863 xref: MESH:D008214 xref: VHOG:0001535 -xref: ZFA:0009250 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009250 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -1240,7 +1245,7 @@ synonym: "GMP" RELATED OMO:0003000 [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC synonym: "granulocyte-macrophage progenitor" EXACT [ISBN:0721601464, PMCID:PMC2213186, PMCID:PMC548021] synonym: "granulocyte/monocyte precursor" EXACT [] synonym: "granulocyte/monocyte progenitor" EXACT [] -xref: ZFA:0009251 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009251 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell @@ -1272,7 +1277,7 @@ subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0004657 xref: FMA:83551 -xref: ZFA:0009253 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell intersection_of: CL:0002194 ! monopoietic cell @@ -1291,7 +1296,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1315,7 +1320,7 @@ subset: human_reference_atlas xref: BTO:0000876 xref: CALOHA:TS-0638 xref: FMA:62864 -xref: ZFA:0009265 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009265 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0011026 ! progenitor cell @@ -1347,7 +1352,7 @@ xref: FMA:63147 xref: FMA:83601 xref: MESH:D007694 xref: VHOG:0001697 -xref: ZFA:0009278 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0001067 ! group 1 innate lymphoid cell intersection_of: CL:0001067 ! group 1 innate lymphoid cell intersection_of: capable_of GO:0002228 ! natural killer cell mediated immunity @@ -1368,7 +1373,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1381,7 +1386,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1394,7 +1399,7 @@ def: "Muscle cell which has as its direct parts myofilaments organized into sarc xref: BTO:0002916 xref: CALOHA:TS-2157 xref: FMA:86936 -xref: ZFA:0005784 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005784 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0001410 ! striated @@ -1417,7 +1422,7 @@ xref: CALOHA:TS-0549 xref: FMA:62852 xref: MESH:D007962 xref: NCIT:C12529 -xref: ZFA:0009309 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009309 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell @@ -1449,7 +1454,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:14067 xref: MESH:D032383 -xref: ZFA:0009316 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009316 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000737 ! striated muscle cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000187 ! muscle cell @@ -1470,7 +1475,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1481,7 +1486,7 @@ id: CL:0000766 name: myeloid leukocyte def: "A cell of the monocyte, granulocyte, or mast cell lineage." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009326 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009326 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte @@ -1516,7 +1521,7 @@ synonym: "NKP" EXACT [PMID:12457618, PMID:15032583, PMID:15766674] synonym: "null cell" RELATED [PMID:11532393] synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] -xref: ZFA:0009348 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein @@ -1550,7 +1555,7 @@ synonym: "progenitor B lymphocyte" EXACT [] synonym: "progenitor B-cell" EXACT [] synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 -xref: ZFA:0009349 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 @@ -1572,7 +1577,7 @@ synonym: "DN1 thymocyte" NARROW [] synonym: "pro-T lymphocyte" EXACT [] synonym: "progenitor T cell" EXACT [] synonym: "TN1 cell" NARROW [] -xref: ZFA:0009350 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009350 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation @@ -1591,7 +1596,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -1638,7 +1643,7 @@ synonym: "lymphoid progenitor cell" BROAD [] xref: BTO:0004731 xref: CALOHA:TS-2025 xref: FMA:70338 -xref: ZFA:0009355 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009355 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1657,7 +1662,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1676,7 +1681,7 @@ synonym: "peripheral blood mononuclear cell" NARROW [] xref: BTO:0000878 xref: CALOHA:TS-0768 xref: FMA:86713 -xref: ZFA:0009357 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009357 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000226 ! single nucleate cell is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte @@ -1704,7 +1709,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1744,8 +1749,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 creation_date: 2011-11-16T04:28:16Z [Term] @@ -1779,7 +1784,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1799,9 +1804,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:20:48Z" xsd:dateTime [Term] id: CL:0001067 @@ -1812,9 +1817,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032609 ! type II interferon production -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 -property_value: http://purl.org/dc/terms/date "2017-01-30T20:42:44Z" xsd:dateTime property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 +property_value: terms:date "2017-01-30T20:42:44Z" xsd:dateTime [Term] id: CL:0002009 @@ -1831,7 +1836,7 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -1845,7 +1850,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1859,7 +1864,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1867,12 +1872,12 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1888,7 +1893,7 @@ is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0002371 ! bone marrow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -1900,7 +1905,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -1912,7 +1917,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1926,7 +1931,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1937,12 +1942,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1952,9 +1957,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1963,7 +1968,7 @@ name: myotube def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] synonym: "myotubule" EXACT [] synonym: "single cell sarcomere" EXACT [] -xref: FBbt:00005812 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000187 ! muscle cell @@ -1971,7 +1976,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere relationship: bearer_of PATO:0002478 ! transversely striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:13:01Z [Term] @@ -1988,7 +1993,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1998,18 +2003,18 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2044,7 +2049,7 @@ relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -2108,7 +2113,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2129,7 +2134,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2140,7 +2145,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2228,6 +2233,18 @@ synonym: "amoeboid cell migration" EXACT [] synonym: "amoeboidal cell migration" EXACT [] is_a: GO:0016477 ! cell migration +[Term] +id: GO:0001677 +name: formation of translation initiation ternary complex +namespace: biological_process +def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd] +synonym: "translation initiation ternary complex assembly" EXACT [] +is_a: GO:0022618 ! protein-RNA complex assembly +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:0044207 ! translation initiation ternary complex +relationship: part_of GO:0006413 ! translational initiation +relationship: results_in_assembly_of GO:0044207 ! translation initiation ternary complex + [Term] id: GO:0001704 name: formation of primary germ layer @@ -2941,6 +2958,79 @@ subset: goslim_prokaryote subset: goslim_yeast is_a: GO:0006259 ! DNA metabolic process +[Term] +id: GO:0006412 +name: translation +namespace: biological_process +alt_id: GO:0006416 +alt_id: GO:0006453 +alt_id: GO:0043037 +def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] +subset: goslim_candida +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_prokaryote +subset: goslim_prokaryote_ribbon +synonym: "protein anabolism" EXACT [] +synonym: "protein biosynthesis" EXACT [] +synonym: "protein biosynthetic process" EXACT [] +synonym: "protein formation" EXACT [] +synonym: "protein synthesis" EXACT [] +synonym: "protein translation" EXACT [] +xref: Wikipedia:Translation_(genetics) +is_a: GO:0009059 ! macromolecule biosynthetic process +is_a: GO:0019538 ! protein metabolic process +relationship: ends_with GO:0006415 ! translational termination +relationship: has_part GO:0006414 ! translational elongation +relationship: part_of GO:0010467 ! gene expression +relationship: starts_with GO:0006413 ! translational initiation + +[Term] +id: GO:0006413 +name: translational initiation +namespace: biological_process +alt_id: GO:0006440 +alt_id: GO:0006454 +def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] +subset: goslim_yeast +synonym: "biopolymerisation" BROAD [] +synonym: "biopolymerization" BROAD [] +synonym: "protein synthesis initiation" BROAD [] +synonym: "translation initiation" EXACT [] +is_a: GO:0044237 ! cellular metabolic process +relationship: part_of GO:0006412 ! translation +relationship: starts_with GO:0001677 ! formation of translation initiation ternary complex + +[Term] +id: GO:0006414 +name: translational elongation +namespace: biological_process +alt_id: GO:0006442 +alt_id: GO:0006455 +def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] +subset: goslim_yeast +synonym: "protein synthesis elongation" BROAD [] +synonym: "translation elongation" EXACT [] +is_a: GO:0009059 ! macromolecule biosynthetic process +relationship: part_of GO:0006412 ! translation + +[Term] +id: GO:0006415 +name: translational termination +namespace: biological_process +alt_id: GO:0006443 +alt_id: GO:0006456 +def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] +synonym: "protein synthesis termination" BROAD [] +synonym: "translation termination" EXACT [] +synonym: "translational complex disassembly" EXACT [] +is_a: GO:0032984 ! protein-containing complex disassembly +relationship: part_of GO:0006412 ! translation + [Term] id: GO:0006810 name: transport @@ -2982,7 +3072,7 @@ name: exocytosis namespace: biological_process alt_id: GO:0016194 alt_id: GO:0016195 -def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] +def: "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." [GOC:mah, ISBN:0716731363, PMID:22323285] subset: goslim_yeast synonym: "nonselective vesicle exocytosis" RELATED [] synonym: "vesicle exocytosis" EXACT [] @@ -3334,7 +3424,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3740,6 +3829,36 @@ relationship: has_part GO:0001508 ! action potential relationship: has_part GO:0007268 ! chemical synaptic transmission relationship: part_of GO:0007154 ! cell communication +[Term] +id: GO:0019538 +name: protein metabolic process +namespace: biological_process +alt_id: GO:0006411 +alt_id: GO:0044267 +alt_id: GO:0044268 +def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: goslim_agr +subset: goslim_flybase_ribbon +subset: goslim_mouse +subset: goslim_pir +subset: goslim_plant +subset: goslim_plant_ribbon +synonym: "cellular protein metabolic process" EXACT [] +synonym: "cellular protein metabolism" EXACT [] +synonym: "multicellular organismal protein metabolic process" NARROW [] +synonym: "protein metabolic process and modification" EXACT [] +synonym: "protein metabolism" EXACT [] +synonym: "protein metabolism and modification" EXACT [] +xref: Wikipedia:Protein_metabolism +is_a: GO:0044238 ! primary metabolic process +intersection_of: GO:0008152 ! metabolic process +intersection_of: has_primary_input_or_output PR:000000001 ! protein +relationship: has_primary_input_or_output PR:000000001 ! protein +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23112" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI + [Term] id: GO:0019724 name: B cell mediated immunity @@ -3781,6 +3900,24 @@ relationship: part_of GO:0007399 ! nervous system development relationship: part_of GO:0043009 ! chordate embryonic development relationship: results_in_development_of UBERON:0001049 ! neural tube +[Term] +id: GO:0022411 +name: cellular component disassembly +namespace: biological_process +alt_id: GO:0071845 +def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] +comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_do_not_annotate +subset: goslim_pir +synonym: "cell structure disassembly" EXACT [] +synonym: "cellular component disassembly at cellular level" EXACT [] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_disassembly_of GO:0005575 ! cellular_component +disjoint_from: GO:0022607 ! cellular component assembly +relationship: results_in_disassembly_of GO:0005575 ! cellular_component +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI + [Term] id: GO:0022414 name: reproductive process @@ -3813,6 +3950,48 @@ intersection_of: GO:0003008 ! system process intersection_of: part_of GO:0007586 ! digestion relationship: part_of GO:0007586 ! digestion +[Term] +id: GO:0022607 +name: cellular component assembly +namespace: biological_process +alt_id: GO:0071844 +def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] +subset: goslim_chembl +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_pir +synonym: "cell structure assembly" EXACT [] +synonym: "cellular component assembly at cellular level" EXACT [] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_assembly_of GO:0005575 ! cellular_component +relationship: part_of GO:0044085 ! cellular component biogenesis +relationship: results_in_assembly_of GO:0005575 ! cellular_component + +[Term] +id: GO:0022613 +name: ribonucleoprotein complex biogenesis +namespace: biological_process +def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex." [GOC:isa_complete, GOC:mah] +synonym: "ribonucleoprotein complex biogenesis and assembly" EXACT [GOC:mah] +synonym: "RNA-protein complex biogenesis" EXACT [GOC:mah] +is_a: GO:0044085 ! cellular component biogenesis + +[Term] +id: GO:0022618 +name: protein-RNA complex assembly +namespace: biological_process +def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl] +subset: goslim_chembl +synonym: "ribonucleoprotein complex assembly" EXACT [] +synonym: "RNA-protein complex assembly" EXACT [] +synonym: "RNP complex assembly" EXACT [] +is_a: GO:0065003 ! protein-containing complex assembly +is_a: GO:0071826 ! protein-RNA complex organization +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex +relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis +relationship: results_in_assembly_of GO:1990904 ! ribonucleoprotein complex + [Term] id: GO:0023052 name: signaling @@ -3875,7 +4054,7 @@ relationship: part_of GO:0030016 ! myofibril id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -3890,7 +4069,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -4237,6 +4416,25 @@ xref: Wikipedia:Secretion is_a: GO:0046903 ! secretion is_a: GO:0140352 ! export from cell +[Term] +id: GO:0032984 +name: protein-containing complex disassembly +namespace: biological_process +alt_id: GO:0034623 +alt_id: GO:0043241 +alt_id: GO:0043624 +def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] +synonym: "cellular macromolecule complex disassembly" RELATED [] +synonym: "cellular protein complex disassembly" RELATED [] +synonym: "macromolecule complex disassembly" RELATED [] +synonym: "protein complex disassembly" EXACT [] +is_a: GO:0022411 ! cellular component disassembly +is_a: GO:0043933 ! protein-containing complex organization +intersection_of: GO:0022411 ! cellular component disassembly +intersection_of: results_in_disassembly_of GO:0032991 ! protein-containing complex +relationship: results_in_disassembly_of GO:0032991 ! protein-containing complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI + [Term] id: GO:0032991 name: protein-containing complex @@ -4443,7 +4641,7 @@ is_a: GO:0042611 ! MHC protein complex id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -4603,6 +4801,53 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27281" xsd:anyURI +[Term] +id: GO:0043933 +name: protein-containing complex organization +namespace: biological_process +alt_id: GO:0034600 +alt_id: GO:0034621 +alt_id: GO:0071822 +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] +synonym: "cellular macromolecular complex organization" RELATED [] +synonym: "cellular macromolecular complex subunit organisation" RELATED [] +synonym: "cellular macromolecular complex subunit organization" RELATED [] +synonym: "macromolecular complex organization" RELATED [] +synonym: "macromolecular complex subunit organisation" RELATED [] +synonym: "macromolecular complex subunit organization" RELATED [] +synonym: "protein complex subunit organisation" EXACT [GOC:mah] +synonym: "protein complex subunit organization" EXACT [] +synonym: "protein-containing complex subunit organization" RELATED [] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0032991 ! protein-containing complex +relationship: results_in_organization_of GO:0032991 ! protein-containing complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI +created_by: mah +creation_date: 2010-09-08T10:01:42Z + +[Term] +id: GO:0044085 +name: cellular component biogenesis +namespace: biological_process +alt_id: GO:0071843 +def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: goslim_pir +synonym: "cellular component biogenesis at cellular level" EXACT [] +is_a: GO:0071840 ! cellular component organization or biogenesis + +[Term] +id: GO:0044207 +name: translation initiation ternary complex +namespace: cellular_component +def: "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:jl] +synonym: "Met-tRNA/eIF2.GTP ternary complex" NARROW [] +synonym: "translation initiation (ternary) complex" EXACT [] +is_a: GO:1990904 ! ribonucleoprotein complex +relationship: part_of GO:0005737 ! cytoplasm +created_by: jl +creation_date: 2009-10-22T02:38:55Z + [Term] id: GO:0044237 name: cellular metabolic process @@ -4615,6 +4860,21 @@ synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process +[Term] +id: GO:0044238 +name: primary metabolic process +namespace: biological_process +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] +subset: gocheck_do_not_annotate +subset: goslim_euk_cellular_processes_ribbon +subset: goslim_pir +subset: goslim_plant_ribbon +subset: goslim_prokaryote_ribbon +synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite +is_a: GO:0008152 ! metabolic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI + [Term] id: GO:0044249 name: cellular biosynthetic process @@ -5330,6 +5590,36 @@ relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z +[Term] +id: GO:0065003 +name: protein-containing complex assembly +namespace: biological_process +alt_id: GO:0006461 +alt_id: GO:0034622 +alt_id: GO:0043623 +def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] +subset: goslim_chembl +subset: goslim_drosophila +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_pombe +subset: goslim_prokaryote +synonym: "cellular macromolecule complex assembly" RELATED [] +synonym: "cellular protein complex assembly" EXACT [] +synonym: "cellular protein-containing complex assembly" RELATED [] +synonym: "chaperone activity" RELATED [] +synonym: "macromolecular complex assembly" RELATED [] +synonym: "macromolecule complex assembly" RELATED [] +synonym: "protein complex assembly" RELATED [] +synonym: "protein complex formation" RELATED [] +is_a: GO:0022607 ! cellular component assembly +is_a: GO:0043933 ! protein-containing complex organization +intersection_of: GO:0022607 ! cellular component assembly +intersection_of: results_in_assembly_of GO:0032991 ! protein-containing complex +relationship: results_in_assembly_of GO:0032991 ! protein-containing complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI + [Term] id: GO:0065007 name: biological regulation @@ -5371,18 +5661,21 @@ intersection_of: GO:0030133 ! transport vesicle intersection_of: capable_of GO:0099500 ! vesicle fusion to plasma membrane [Term] -id: GO:0071704 -name: organic substance metabolic process +id: GO:0071826 +name: protein-RNA complex organization namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI +def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex." [GOC:mah] +synonym: "protein-RNA complex subunit organization" EXACT [GOC:mah] +synonym: "ribonucleoprotein complex subunit organisation" EXACT [GOC:mah] +synonym: "ribonucleoprotein complex subunit organization" EXACT [] +synonym: "RNA-protein complex subunit organization" EXACT [GOC:mah] +is_a: GO:0043933 ! protein-containing complex organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:1990904 ! ribonucleoprotein complex +relationship: results_in_organization_of GO:1990904 ! ribonucleoprotein complex +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25143" xsd:anyURI created_by: mah -creation_date: 2010-03-08T03:32:18Z +creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 @@ -5774,27 +6067,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2020-11-11T17:19:06Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1902105 name: regulation of leukocyte differentiation @@ -5840,6 +6112,24 @@ relationship: regulates GO:0030097 ! hemopoiesis created_by: pad creation_date: 2014-12-04T15:34:13Z +[Term] +id: GO:1990904 +name: ribonucleoprotein complex +namespace: cellular_component +alt_id: GO:0030529 +alt_id: GO:1990903 +def: "A macromolecular complex that contains both RNA and protein molecules." [GOC:krc, GOC:vesicles] +subset: goslim_pir +synonym: "extracellular ribonucleoprotein complex" NARROW [] +synonym: "intracellular ribonucleoprotein complex" NARROW [] +synonym: "protein-RNA complex" EXACT [] +synonym: "RNA-protein complex" EXACT [] +synonym: "RNP" EXACT [] +xref: Wikipedia:Ribonucleoprotein +is_a: GO:0032991 ! protein-containing complex +created_by: pr +creation_date: 2015-11-19T12:26:37Z + [Term] id: GO:2000026 name: regulation of multicellular organismal development @@ -6415,7 +6705,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6427,7 +6717,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6437,7 +6727,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6447,7 +6737,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6456,7 +6746,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6469,7 +6759,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6480,7 +6770,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6490,7 +6780,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6502,7 +6792,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:15Z [Term] @@ -6513,7 +6803,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6522,7 +6812,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6576,6 +6866,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -7255,6 +7548,15 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -7306,6 +7608,18 @@ synonym: "CD45R" EXACT [] synonym: "PTPRC/iso:CD45R" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -7342,7 +7656,7 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005155 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7357,7 +7671,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7407,7 +7721,7 @@ relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002176 UBERON:0001474 ! connects bone element relationship: RO:0002176 UBERON:0001630 ! connects muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI [Term] id: UBERON:0000058 @@ -7420,7 +7734,7 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7466,7 +7780,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7785,7 +8099,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -7887,7 +8201,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -7911,7 +8225,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -7934,7 +8248,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -7994,7 +8308,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8029,7 +8343,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8057,7 +8371,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8082,7 +8396,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8119,7 +8433,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -8173,7 +8487,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8217,7 +8531,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8253,7 +8567,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8273,7 +8587,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -8299,7 +8613,7 @@ xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 -xref: FBbt:00005835 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005835 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 @@ -8335,7 +8649,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8370,7 +8684,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8403,7 +8717,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8426,7 +8740,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000486 @@ -8502,7 +8816,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -8523,7 +8837,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -8543,7 +8857,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8577,7 +8891,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8595,7 +8909,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8615,7 +8929,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8632,8 +8946,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8659,7 +8973,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8676,7 +8990,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -8699,7 +9013,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8712,7 +9026,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -8733,7 +9047,7 @@ xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 -xref: FBbt:00005068 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005068 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9668 xref: GAID:439 xref: MA:0000012 @@ -8778,7 +9092,7 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005162 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -8851,7 +9165,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -8905,7 +9219,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -8944,7 +9258,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -8970,7 +9284,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9000,8 +9314,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -9032,7 +9346,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9078,7 +9392,7 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007692 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9093,7 +9407,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001049 @@ -9132,7 +9446,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9148,7 +9462,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9241,7 +9555,7 @@ intersection_of: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle f relationship: part_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: RO:0002202 UBERON:0003082 ! develops from myotome relationship: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string [Term] @@ -9356,7 +9670,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -9447,7 +9761,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -9619,7 +9933,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -9660,7 +9974,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -9727,8 +10041,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -9751,7 +10065,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -9826,7 +10140,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0000949 ! endocrine system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI [Term] id: UBERON:0002371 @@ -9871,7 +10185,7 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -10070,7 +10384,7 @@ xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 xref: EMAPA:18425 -xref: FBbt:00100317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7146 xref: FMA:86294 xref: galen:Gland @@ -10087,7 +10401,7 @@ is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: produces UBERON:0000463 ! organism substance relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] id: UBERON:0002532 @@ -10111,7 +10425,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -10210,7 +10524,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -10245,7 +10559,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -10276,7 +10590,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -10311,7 +10625,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003082 @@ -10348,7 +10662,7 @@ xref: ZFA:0001056 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome relationship: RO:0002433 UBERON:0001630 ! contributes to morphology of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI property_value: IAO:0000116 "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string [Term] @@ -10405,7 +10719,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -10434,7 +10748,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -10598,7 +10912,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -10696,7 +11010,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -10712,7 +11026,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -10848,7 +11162,7 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004200 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000970 ! eye @@ -10868,7 +11182,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -11253,7 +11567,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -11323,7 +11637,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -11549,7 +11863,7 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007278 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -11702,7 +12016,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -11759,8 +12073,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Term] id: UBERON:8600006 @@ -11770,8 +12084,8 @@ def: "A striated muscle tissue that is associated with soft internal organs (vis synonym: "striated visceral muscle tissue" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:8600004 ! visceral muscle tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:34:43Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:34:43Z" xsd:dateTime [Typedef] id: BFO:0000067 @@ -12842,8 +13156,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -12851,8 +13165,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -12861,8 +13175,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -13013,16 +13327,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -13031,6 +13349,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -13048,6 +13367,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -13266,6 +13586,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -13724,18 +14045,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/subsets/general_cell_types_upper_slim.owl b/subsets/general_cell_types_upper_slim.owl index 7d5d68045..4354de63c 100644 --- a/subsets/general_cell_types_upper_slim.owl +++ b/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4506,6 +4512,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4517,6 +4525,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4527,6 +4536,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4539,6 +4549,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4557,6 +4568,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4586,6 +4598,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4694,6 +4707,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4705,6 +4719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4716,6 +4731,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -10052,7 +10068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A connective tissue cell found in bone. - 2011-11-16T04:28:16Z + 2011-11-16T04:28:16Z bone cell @@ -10204,7 +10220,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z hematopoietic oligopotent progenitor cell, lineage-negative @@ -10369,7 +10385,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. - 2010-01-19T02:51:58Z + 2010-01-19T02:51:58Z MDP macrophage dendritic cell progenitor @@ -10420,7 +10436,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -10463,7 +10479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -10502,7 +10518,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -10546,7 +10562,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. - 2010-07-22T04:48:15Z + 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 MESH:D001854 @@ -10593,7 +10609,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell involved in the formation of a monocyte (monopoiesis). - 2010-08-30T01:27:48Z + 2010-08-30T01:27:48Z FMA:83552 monopoietic cell @@ -10635,7 +10651,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -10671,7 +10687,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -10710,7 +10726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -10740,7 +10756,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -10794,7 +10810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. - 2010-09-24T01:13:01Z + 2010-09-24T01:13:01Z FBbt:00005812 myotubule single cell sarcomere @@ -10841,7 +10857,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -10865,7 +10881,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). - 2012-06-15T02:51:27Z + 2012-06-15T02:51:27Z scleroblast Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell @@ -10903,7 +10919,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -11264,7 +11280,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. - 2010-05-25T01:36:34Z + 2010-05-25T01:36:34Z neutrophillic cytoplasm @@ -11299,7 +11315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -11507,6 +11523,48 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + translation initiation ternary complex assembly + biological_process + GO:0001677 + formation of translation initiation ternary complex + + + + + Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + GOC:hjd + + + + @@ -12821,32 +12879,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -13358,6 +13416,164 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. + GO:0006416 + GO:0006453 + GO:0043037 + Wikipedia:Translation_(genetics) + protein anabolism + protein biosynthesis + protein biosynthetic process + protein formation + protein synthesis + protein translation + biological_process + GO:0006412 + + + + + + + + + + translation + + + + + The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. + GOC:go_curators + + + + + + + + + + + + + + + + + + + + + The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. + GO:0006440 + GO:0006454 + biopolymerisation + biopolymerization + protein synthesis initiation + translation initiation + biological_process + GO:0006413 + + translational initiation + + + + + The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA. + ISBN:019879276X + + + + + + + + + + + + + + + The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. + GO:0006442 + GO:0006455 + protein synthesis elongation + translation elongation + biological_process + GO:0006414 + + translational elongation + + + + + The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. + GOC:ems + + + + + + + + + + + + + + + The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). + GO:0006443 + GO:0006456 + protein synthesis termination + translation termination + translational complex disassembly + biological_process + GO:0006415 + translational termination + + + + + The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). + GOC:hjd + ISBN:019879276X + + + + @@ -13446,7 +13662,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GO:0016194 GO:0016195 Wikipedia:Exocytosis @@ -13460,7 +13676,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. + A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for example of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell. GOC:mah ISBN:0716731363 PMID:22323285 @@ -14245,7 +14461,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -15265,6 +15480,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + The chemical reactions and pathways involving a protein. Includes protein modification. + https://github.com/geneontology/go-ontology/issues/23112 + https://github.com/geneontology/go-ontology/issues/27189 + GO:0006411 + GO:0044267 + GO:0044268 + Wikipedia:Protein_metabolism + cellular protein metabolic process + cellular protein metabolism + protein metabolic process and modification + protein metabolism + protein metabolism and modification + multicellular organismal protein metabolic process + biological_process + GO:0019538 + + + + + + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + protein metabolic process + + + + + The chemical reactions and pathways involving a protein. Includes protein modification. + GOC:ma + + + + @@ -15387,6 +15657,49 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + A cellular process that results in the breakdown of a cellular component. + https://github.com/geneontology/go-ontology/issues/27189 + GO:0071845 + cell structure disassembly + cellular component disassembly at cellular level + biological_process + GO:0022411 + + + Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. + cellular component disassembly + + + + + A cellular process that results in the breakdown of a cellular component. + GOC:isa_complete + + + + @@ -15458,6 +15771,132 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + The aggregation, arrangement and bonding together of a cellular component. + GO:0071844 + cell structure assembly + cellular component assembly at cellular level + biological_process + GO:0022607 + + + + cellular component assembly + + + + + The aggregation, arrangement and bonding together of a cellular component. + GOC:isa_complete + + + + + + + + + A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. + RNA-protein complex biogenesis + ribonucleoprotein complex biogenesis and assembly + biological_process + GO:0022613 + ribonucleoprotein complex biogenesis + + + + + A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex. + GOC:isa_complete + GOC:mah + + + + + RNA-protein complex biogenesis + GOC:mah + + + + + ribonucleoprotein complex biogenesis and assembly + GOC:mah + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. + RNA-protein complex assembly + RNP complex assembly + ribonucleoprotein complex assembly + biological_process + GO:0022618 + + protein-RNA complex assembly + + + + + The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex. + GOC:jl + + + + @@ -15644,7 +16083,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -15685,7 +16124,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -16566,6 +17004,50 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The disaggregation of a protein-containing macromolecular complex into its constituent components. + https://github.com/geneontology/go-ontology/issues/22580 + GO:0034623 + GO:0043241 + GO:0043624 + protein complex disassembly + biological_process + cellular macromolecule complex disassembly + cellular protein complex disassembly + macromolecule complex disassembly + GO:0032984 + protein-containing complex disassembly + + + + + The disaggregation of a protein-containing macromolecular complex into its constituent components. + GOC:mah + + + + @@ -17172,7 +17654,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -17568,6 +18050,112 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. + https://github.com/geneontology/go-ontology/issues/22580 + mah + 2010-09-08T10:01:42Z + GO:0034600 + GO:0034621 + GO:0071822 + protein complex subunit organisation + protein complex subunit organization + biological_process + cellular macromolecular complex organization + cellular macromolecular complex subunit organisation + cellular macromolecular complex subunit organization + macromolecular complex organization + macromolecular complex subunit organisation + macromolecular complex subunit organization + protein-containing complex subunit organization + GO:0043933 + protein-containing complex organization + + + + + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. + GOC:mah + + + + + protein complex subunit organisation + GOC:mah + + + + + + + + + A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + GO:0071843 + cellular component biogenesis at cellular level + biological_process + GO:0044085 + + cellular component biogenesis + + + + + A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + GOC:jl + GOC:mah + + + + + + + + + + + + + + + A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + jl + 2009-10-22T02:38:55Z + translation initiation (ternary) complex + Met-tRNA/eIF2.GTP ternary complex + cellular_component + GO:0044207 + translation initiation ternary complex + + + + + A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator). + GOC:jl + + + + @@ -17597,6 +18185,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. + https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite + primary metabolism + biological_process + GO:0044238 + + + + + + primary metabolic process + + + + + The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. + GOC:go_curators + + + + @@ -19557,6 +20171,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. + https://github.com/geneontology/go-ontology/issues/22580 + GO:0006461 + GO:0034622 + GO:0043623 + cellular protein complex assembly + biological_process + cellular macromolecule complex assembly + cellular protein-containing complex assembly + chaperone activity + macromolecular complex assembly + macromolecule complex assembly + protein complex assembly + protein complex formation + GO:0065003 + + + + + + + + protein-containing complex assembly + + + + + The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. + GOC:jl + + + + @@ -19681,26 +20350,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 + + + + + + + + + + + + + + + + + + + + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. + https://github.com/geneontology/go-ontology/issues/25143 mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism + 2010-09-08T10:10:35Z + RNA-protein complex subunit organization + protein-RNA complex subunit organization + ribonucleoprotein complex subunit organisation + ribonucleoprotein complex subunit organization biological_process - GO:0071704 - - organic substance metabolic process + GO:0071826 + protein-RNA complex organization - + - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. + Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex. + GOC:mah + + + + + RNA-protein complex subunit organization + GOC:mah + + + + + protein-RNA complex subunit organization + GOC:mah + + + + + ribonucleoprotein complex subunit organisation GOC:mah @@ -20852,63 +21556,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -21073,6 +21720,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A macromolecular complex that contains both RNA and protein molecules. + pr + 2015-11-19T12:26:37Z + GO:0030529 + GO:1990903 + Wikipedia:Ribonucleoprotein + RNA-protein complex + RNP + protein-RNA complex + extracellular ribonucleoprotein complex + intracellular ribonucleoprotein complex + cellular_component + GO:1990904 + + ribonucleoprotein complex + + + + + A macromolecular complex that contains both RNA and protein molecules. + GOC:krc + GOC:vesicles + + + + @@ -22739,6 +23416,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -24550,6 +25235,39 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -24724,6 +25442,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -24927,8 +25697,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -24976,11 +25746,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -24993,13 +25763,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + AEO @@ -25904,7 +26674,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25940,14 +26710,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -27354,7 +28124,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27396,14 +28166,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27746,7 +28516,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27781,14 +28551,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27828,7 +28598,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27863,14 +28633,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27911,7 +28681,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27952,14 +28722,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28215,8 +28985,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -28248,24 +29018,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -28659,7 +29429,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28711,14 +29481,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -28784,7 +29554,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -28829,7 +29599,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -28843,7 +29613,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -29563,7 +30333,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Skeletal element that is composed of bone tissue. @@ -29605,14 +30375,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -29678,7 +30448,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -29715,14 +30485,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -30251,9 +31021,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -30301,15 +31071,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -30328,19 +31098,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -30380,8 +31150,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -30419,11 +31189,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -30436,13 +31206,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -30567,22 +31337,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -30615,45 +31385,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -30960,7 +31730,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31016,14 +31786,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -31235,7 +32005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31289,14 +32059,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -31706,7 +32476,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -31729,14 +32499,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -31890,9 +32660,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -31921,34 +32691,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -31988,7 +32758,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -32014,7 +32784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32027,7 +32797,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -32074,7 +32844,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32114,7 +32884,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32127,7 +32897,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -32177,7 +32947,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32218,7 +32988,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -32231,7 +33001,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2-abduced @@ -32391,7 +33161,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -32406,14 +33176,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -32715,7 +33485,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The bilaminar epithelium formed from the myotome and dermatome. AAO:0010572 AEO:0000214 @@ -32733,7 +33503,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004290 dermomyotome - + @@ -32752,7 +33522,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 ZFA @@ -33083,7 +33853,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -33097,14 +33867,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -33131,7 +33901,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33170,14 +33940,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -33618,7 +34388,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -33634,14 +34404,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -33950,7 +34720,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -33964,7 +34734,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -33977,7 +34747,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -34005,7 +34775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -34022,14 +34792,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -34640,7 +35410,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34666,7 +35436,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -34682,7 +35452,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -34731,7 +35501,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -34739,7 +35509,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -34752,7 +35522,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -34910,7 +35680,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34927,14 +35697,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -34956,7 +35726,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -34964,14 +35734,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -35451,7 +36221,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35475,7 +36245,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0011899 epimysium - + @@ -35488,7 +36258,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -35594,7 +36364,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35615,7 +36385,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -35628,7 +36398,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -36183,7 +36953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36206,7 +36976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -36219,7 +36989,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -36305,7 +37075,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36322,14 +37092,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal musculature - + - + MA @@ -36882,5 +37652,5 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + diff --git a/subsets/general_cell_types_upper_slim.tsv b/subsets/general_cell_types_upper_slim.tsv index df42d0949..e12af28b8 100644 --- a/subsets/general_cell_types_upper_slim.tsv +++ b/subsets/general_cell_types_upper_slim.tsv @@ -1,270 +1,279 @@ ?x ?label -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1005 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1012 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1018 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1059 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1074 -_:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid1080 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+_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid864 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid874 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid901 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid918 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid927 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid977 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid985 +_:B1f53bb67X2D880dX2D461cX2D942fX2D7b26c38ff17egenid993 "cell" "neuronal receptor cell" "early embryonic cell (metazoa)" @@ -400,6 +409,7 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "heterochromatin" "action potential" "ameboidal-type cell migration" + "formation of translation initiation ternary complex" "formation of primary germ layer" "ectoderm formation" "endoderm formation" @@ -452,6 +462,10 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "cell-cell junction" "DNA metabolic process" "DNA recombination" + "translation" + "translational initiation" + "translational elongation" + "translational termination" "transport" "monoatomic ion transport" "exocytosis" @@ -511,11 +525,16 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "cell migration" "stem cell division" "transmission of nerve impulse" + "protein metabolic process" "B cell mediated immunity" "antigen processing and presentation" "neural tube development" + "cellular component disassembly" "reproductive process" "digestive system process" + "cellular component assembly" + "ribonucleoprotein complex biogenesis" + "protein-RNA complex assembly" "signaling" "signal release" "myofibril" @@ -546,6 +565,7 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "developmental process" "type II interferon production" "secretion by cell" + "protein-containing complex disassembly" "protein-containing complex" "protein-DNA complex" "V(D)J recombination" @@ -576,7 +596,11 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "intracellular non-membrane-bounded organelle" "organelle lumen" "contractile muscle fiber" + "protein-containing complex organization" + "cellular component biogenesis" + "translation initiation ternary complex" "cellular metabolic process" + "primary metabolic process" "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" "innate immune response" @@ -633,11 +657,12 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "membrane organization" "membrane fusion" "collagen-containing extracellular matrix" + "protein-containing complex assembly" "biological regulation" "intracellular organelle lumen" "anchoring junction" "exocytic vesicle" - "organic substance metabolic process" + "protein-RNA complex organization" "cellular component organization or biogenesis" "cell periphery" "elastic fiber" @@ -671,10 +696,10 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "exocytic process" "export from cell" "defense response to symbiont" - "organic substance biosynthetic process" "regulation of leukocyte differentiation" "mononuclear cell differentiation" "regulation of hemopoiesis" + "ribonucleoprotein complex" "regulation of multicellular organismal development" "root" "Muridae" @@ -800,11 +825,13 @@ _:Bfac34fc2X2D25bfX2D4635X2Db891X2D94da1b8803a5genid993 "nuclear factor NF-kappa-B p100 subunit" "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "eukaryotic protein" "cathepsin-like protease" "receptor-type tyrosine-protein phosphatase C isoform CD45R" + "protein-containing molecular entity" "processual entity" "sense organ" "tube" diff --git a/subsets/kidney_upper_slim.json b/subsets/kidney_upper_slim.json index 083c32f0b..a1c0d3fe7 100644 --- a/subsets/kidney_upper_slim.json +++ b/subsets/kidney_upper_slim.json @@ -4,164 +4,11 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-05-15" + "val" : "2024-07-10" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-05-15/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-07-10/subsets/kidney_upper_slim.owl" }, "nodes" : [ { - "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a part and its whole" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000050" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a core relation that holds between a whole and its part" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000051" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_part" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000062", - "lbl" : "preceded by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000062" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preceded_by" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000063", - "lbl" : "precedes", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "BFO:0000063" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "precedes" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000066", - "lbl" : "occurs in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], - "xrefs" : [ { - "val" : "BFO:0000066" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Occurs_in" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000067", - "lbl" : "contains process", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" - }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] - } - }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", "type" : "CLASS", @@ -548,24 +395,6 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000064", - "lbl" : "ciliated cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell that has a filiform extrusion of the cell surface.", - "xrefs" : [ "GOC:tfm" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "xrefs" : [ { - "val" : "VHOG:0001532" - }, { - "val" : "XAO:0000031" - }, { - "val" : "ZFA:0009032" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000066", "lbl" : "epithelial cell", @@ -603,22 +432,6 @@ "val" : "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000067", - "lbl" : "ciliated epithelial cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An epithelial cell that has a cilia.", - "xrefs" : [ "GOC:tfm" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "xrefs" : [ { - "val" : "FMA:70605" - }, { - "val" : "ZFA:0009035" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000068", "lbl" : "duct epithelial cell", @@ -643,10 +456,6 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cuboidal endothelial cell of vascular tree" - } ], "xrefs" : [ { "val" : "ZFA:0009036" } ], @@ -1084,15 +893,6 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000239", - "lbl" : "brush border epithelial cell", - "type" : "CLASS", - "meta" : { - "xrefs" : [ { - "val" : "ZFA:0009143" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000255", "lbl" : "eukaryotic cell", @@ -1627,9 +1427,13 @@ } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000666", - "lbl" : "fenestrated cell", + "lbl" : "fenestrated endothelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues.", + "xrefs" : [ "DOI:10.1007/978-3-211-99390-3_133" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -2101,6 +1905,7 @@ "val" : "An epithelial cell of the proximal tubule of the kidney.", "xrefs" : [ "GOC:tfm", "ISBN:1-4160-2328-3" ] }, + "comments" : [ "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -2968,30 +2773,6 @@ "val" : "2022-11-30T14:35:08Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030044", - "lbl" : "has_not_completed", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030045", - "lbl" : "lacks_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_4030046", - "lbl" : "lacks_plasma_membrane_part", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_4033054", "lbl" : "perivascular cell", @@ -3009,68 +2790,6 @@ "val" : "2023-08-22T13:40:28Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", - "lbl" : "results_in_distribution_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002003" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_distribution_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", - "lbl" : "results_in_fission_of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "GOREL:0002004" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "results_in_fission_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0000226", - "lbl" : "microtubule cytoskeleton organization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pombe" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "microtubule cytoskeleton organisation", - "xrefs" : [ "GOC:mah" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "microtubule cytoskeleton organization and biogenesis", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23114" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/23195" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -3078,7 +2797,7 @@ "meta" : { "definition" : { "val" : "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.", - "xrefs" : [ "GOC:mah", "ISBN:0815316194", "Reactome:69278" ] + "xrefs" : [ "GOC:mah", "ISBN:0815316194" ] }, "comments" : [ "Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], @@ -3209,24 +2928,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0001578", - "lbl" : "microtubule bundle formation", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process that results in a parallel arrangement of microtubules.", - "xrefs" : [ "GOC:dph" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "microtubule bundling" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0001677", "lbl" : "formation of translation initiation ternary complex", @@ -4081,85 +3782,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005773", - "lbl" : "vacuole", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.", - "xrefs" : [ "GOC:mtg_sensu", "ISBN:0198506732" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "vacuolar carboxypeptidase Y" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Vacuole" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005794", - "lbl" : "Golgi apparatus", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.", - "xrefs" : [ "ISBN:0198506732" ] - }, - "comments" : [ "Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "Golgi" - }, { - "pred" : "hasExactSynonym", - "val" : "Golgi complex" - }, { - "pred" : "hasNarrowSynonym", - "val" : "Golgi ribbon" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao451912436" - }, { - "val" : "Wikipedia:Golgi_apparatus" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005798", - "lbl" : "Golgi-associated vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this definition includes vesicles that are transiently associated with the Golgi." ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "Golgi vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vesicular component", - "xrefs" : [ "NIF_Subcellular:sao138219748" ] - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao819927218" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0005840", "lbl" : "ribosome", @@ -4195,55 +3817,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0005856", - "lbl" : "cytoskeleton", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. 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The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. 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The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. 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Docking requires only that the proteins come close enough to interact and adhere.", - "xrefs" : [ "GOC:isa_complete", "PMID:27875684" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0022411", "lbl" : "cellular component disassembly", @@ -6510,7 +5795,7 @@ "meta" : { "definition" : { "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_prokaryote" ], "synonyms" : [ { @@ -6540,7 +5825,7 @@ "meta" : { "definition" : { "val" : "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "GOC:mah", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "GOC:mah", "PMID:18391171" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", @@ -6562,7 +5847,7 @@ "meta" : { "definition" : { "val" : "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella.", - "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264", "http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html" ] + "xrefs" : [ "GOC:aruk", "GOC:bc", "GOC:mah", "ISBN:0198506732", "PMID:26820516", "PMID:28096264" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon" ], "xrefs" : [ { @@ -6780,47 +6065,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030705", - "lbl" : "cytoskeleton-dependent intracellular transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.", - "xrefs" : [ "GOC:mah" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0030990", - "lbl" : "intraciliary transport particle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules.", - "xrefs" : [ "GOC:cilia", "GOC:kmv", "PMID:14570576", "PMID:22118932", "PMID:23945166" ] - }, - "comments" : [ "Note that we deem cilia and microtubule-based flagella to be equivalent." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport complex" - }, { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport particle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "IFT complex" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0031012", "lbl" : "extracellular matrix", @@ -6851,81 +6095,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031410", - "lbl" : "cytoplasmic vesicle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A vesicle found in the cytoplasm of a cell.", - "xrefs" : [ "GOC:ai", "GOC:mah", "GOC:vesicles" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_generic", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_yeast" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane bounded vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic membrane-enclosed vesicle" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cytoplasmic, membrane-bounded vesicle" - } ], - "xrefs" : [ { - "val" : "NIF_Subcellular:sao180601769" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0016023" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0031503", - "lbl" : "protein-containing complex localization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.", - "xrefs" : [ "GOC:mah" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "establishment and maintenance of protein complex localization" - 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} }, { "id" : "http://purl.obolibrary.org/obo/GO_0031974", "lbl" : "membrane-enclosed lumen", @@ -7122,20 +6291,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032838", - "lbl" : "plasma membrane bounded cell projection cytoplasm", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection.", - "xrefs" : [ "GOC:krc", "GOC:mah" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0032940", "lbl" : "secretion by cell", @@ -7272,29 +6427,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0033365", - "lbl" : "protein localization to organelle", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process in which a protein is transported to, or maintained in, a location within an organelle.", - 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"comments" : [ "Note that cilia and eukaryotic flagella are deemed to be equivalent." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ciliary axoneme assembly" - }, { - "pred" : "hasExactSynonym", - "val" : "cilium axoneme assembly" - }, { - "pred" : "hasExactSynonym", - "val" : "flagellar axoneme assembly" - }, { - "pred" : "hasExactSynonym", - "val" : "flagellum axoneme assembly" - }, { - "pred" : "hasRelatedSynonym", - "val" : "axoneme biogenesis", - "xrefs" : [ "GOC:mah" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "cilium axoneme biogenesis", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035083" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035084" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0035148", "lbl" : "tube formation", @@ -7471,70 +6561,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0035735", - "lbl" : "intraciliary transport involved in cilium assembly", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly.", - "xrefs" : [ "GOC:bf", "GOC:cilia", "Reactome:R-HSA-5620924.2" ] - }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "intraflagellar transport" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intraciliary transport involved in cilium morphogenesis" - }, { - "pred" : "hasRelatedSynonym", - "val" : "intraflagellar transport involved in cilium morphogenesis" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-5620924.2" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-03-17T10:55:42Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0035869", - "lbl" : "ciliary transition zone", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. 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Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cilial transition zone" - }, { - "pred" : "hasExactSynonym", - "val" : "cilium transition zone" - }, { - "pred" : "hasRelatedSynonym", - "val" : "connecting cilium" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "bf" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-05-25T03:09:58Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0040011", "lbl" : "locomotion", @@ -7582,58 +6608,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0042073", - "lbl" : "intraciliary transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins.", - "xrefs" : [ "GOC:cilia", "GOC:kmv", "PMID:17981739", "PMID:18180368", "PMID:22869374", "Reactome:R-HSA-5620924.2" ] - }, - "comments" : [ "Note that we deem cilium and microtubule-based flagellum to be equivalent." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport" - }, { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport involved in cilium organization" - }, { - "pred" : "hasExactSynonym", - "val" : "intraflagellar transport involved in microtubule-based flagellum organisation" - }, { - "pred" : "hasRelatedSynonym", - "val" : "IFT" - } ], - "xrefs" : [ { - "val" : "Wikipedia:Intraflagellar_transport" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3176" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3312" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3378" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_3398" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4890" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_5782" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0035734" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0042391", "lbl" : "regulation of membrane potential", @@ -7698,7 +6672,7 @@ "meta" : { "definition" : { "val" : "A prolongation or process extending from a cell, e.g. a flagellum or axon.", - "xrefs" : [ "GOC:jl", "http://www.cogsci.princeton.edu/~wn/" ] + "xrefs" : [ "GOC:jl", "PMID:16318917" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_agr", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", "http://purl.obolibrary.org/obo/go#goslim_mouse", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_prokaryote", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { @@ -8096,13 +7070,16 @@ "meta" : { "definition" : { "val" : "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.", - "xrefs" : [ "GOC:go_curators", "http://www.metacyc.org" ] + "xrefs" : [ "GOC:go_curators" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", "http://purl.obolibrary.org/obo/go#goslim_pir", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "primary metabolism" } ], + "xrefs" : [ { + "val" : "Wikipedia:Primary_metabolite" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/26424" @@ -8143,32 +7120,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0044782", - "lbl" : "cilium organization", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. 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Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). 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In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane.", - "xrefs" : [ "GOC:cilia", "PMID:13978319", "PMID:23348840", "PMID:23530209", "PMID:25686250", "PMID:26981235", "Reactome:R-HSA-5620912.1" ] - }, - "comments" : [ "Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ciliary basal body docking" - }, { - "pred" : "hasRelatedSynonym", - "val" : "anchoring of the basal body to the plasma membrane" - } ], - "xrefs" : [ { - "val" : "Reactome:R-HSA-5620912.1" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-08-05T16:12:33Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0097712", - "lbl" : "vesicle targeting, trans-Golgi to periciliary membrane compartment", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces.", - "xrefs" : [ "GOC:cilia", "PMID:20106869", "PMID:23351793", "PMID:24814148", "PMID:26485645", "Reactome:R-HSA-5620920.1" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-08-05T16:16:28Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0097734", "lbl" : "extracellular exosome biogenesis", @@ -10321,55 +8781,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099111", - "lbl" : "microtubule-based transport", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.", - "xrefs" : [ "GOC:cjm", "ISBN:0815316194" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099512", - "lbl" : "supramolecular fiber", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.", - "xrefs" : [ "GOC:dos" ] - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "fibril" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "GO:0043205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099513", - "lbl" : "polymeric cytoskeletal fiber", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits.", - "xrefs" : [ "GOC:dos" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0099536", "lbl" : "synaptic signaling", @@ -10400,21 +8811,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0099568", - "lbl" : "cytoplasmic region", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm.", - "xrefs" : [ "GOC:dos" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0110165", "lbl" : "cellular anatomical entity", @@ -10544,27 +8940,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0140056", - "lbl" : "organelle localization by membrane tethering", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other.", - "xrefs" : [ "PMID:27875684" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pombe" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pg" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2017-06-27T09:58:51Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140112", "lbl" : "extracellular vesicle biogenesis", @@ -10616,62 +8991,6 @@ "val" : "biological_process" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1901576", - "lbl" : "organic substance biosynthetic process", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.", - "xrefs" : [ "GOC:TermGenie", "GOC:pr" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity anabolism", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity biosynthetic process" - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic molecular entity synthesis", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance anabolism" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance biosynthesis" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance formation" - }, { - "pred" : "hasExactSynonym", - "val" : "organic substance synthesis" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/geneontology/go-ontology/issues/26424" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2012-11-05T11:04:40Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1903047", "lbl" : "mitotic cell cycle process", @@ -10718,47 +9037,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_1905349", - "lbl" : "ciliary transition zone assembly", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone.", - "xrefs" : [ "GOC:TermGenie", "GOC:cilia", "GO_REF:0000079", "PMID:21725307", "PMID:23644468", "PMID:24448408", "PMID:26595381", "PMID:26982032" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cilial transition zone assembly", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cilial transition zone formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "ciliary transition zone formation", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cilium transition zone assembly", - "xrefs" : [ "GOC:TermGenie" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cilium transition zone formation", - "xrefs" : [ "GOC:TermGenie" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "pr" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2016-08-04T14:49:43Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "biological_process" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_1990904", "lbl" : "ribonucleoprotein complex", @@ -10805,260 +9083,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000002", - "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000028", - "lbl" : "symbol", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000103", - "lbl" : "failed exploratory term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000116", - "lbl" : "editor note", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000120", - "lbl" : "metadata complete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000121", - "lbl" : "organizational term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000122", - "lbl" : "ready for release", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000123", - "lbl" : "metadata incomplete", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000124", - "lbl" : "uncurated", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000125", - "lbl" : "pending final vetting", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000226", - "lbl" : "placeholder removed", - "type" : "INDIVIDUAL" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000227", - "lbl" : "terms merged", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "An editor note should explain what were the merged terms and the reason for the merge." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000228", - "lbl" : "term imported", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000229", - "lbl" : "term split", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000231", - "lbl" : "has obsolescence reason", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000233", - "lbl" : "term tracker item", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "An IRI or similar locator for a request or discussion of an ontology term." - }, - "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], - "xrefs" : [ { - "val" : "IAO:0000233" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "term_tracker_item" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000410", - "lbl" : "universal", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000420", - "lbl" : "defined class", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000421", - "lbl" : "named class expression", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000423", - "lbl" : "to be replaced with external ontology term", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "Terms with this status should eventually replaced with a term from another ontology." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000424", - "lbl" : "expand expression to", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000428", - "lbl" : "requires discussion", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000700", - "lbl" : "preferred_root", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." - }, - "xrefs" : [ { - "val" : "IAO:0000700" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_ontology_root_term" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0100001", - "lbl" : "term replaced by", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" - }, - "comments" : [ "Add as annotation triples in the granting ontology" ] - } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", "lbl" : "root", @@ -11727,73 +9751,6 @@ "val" : "ncbi_taxonomy" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0001000", - "lbl" : "out of scope", - "type" : "INDIVIDUAL", - "meta" : { - "definition" : { - "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0002000", - "lbl" : "defined by construct", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/ontodev/robot/issues/963" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-7356-1779" - }, { - "pred" : "http://purl.org/dc/elements/1.1/contributor", - "val" : "https://orcid.org/0000-0002-8688-6599" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003000", - "lbl" : "abbreviation", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing abbreviations or initalisms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMO_0003004", - "lbl" : "plural form", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "A synonym type for describing pluralization synonyms" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-4423-4370" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", @@ -12433,6 +10390,27 @@ "val" : "quality" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PATO_0002064", + "lbl" : "fenestrated", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes.", + "xrefs" : [ "PATOC:me" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/pato#cell_quality", "http://purl.obolibrary.org/obo/pato#mpath_slim", "http://purl.obolibrary.org/obo/pato#value_slim" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-2061-091X" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2009-07-01T01:46:53Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002078", "lbl" : "hollow", @@ -12517,27 +10495,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002226", - "lbl" : "subcylindrical", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical.", - "xrefs" : [ "url:http://www.thefreedictionary.com/Subcylindrical" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-2061-091X" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2010-07-13T04:22:30Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002266", "lbl" : "3-D shape", @@ -12588,28 +10545,6 @@ "val" : "quality" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/PATO_0002309", - "lbl" : "fiber shaped", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter.", - "xrefs" : [ "PATOC:DC" ] - }, - "comments" : [ "Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope)." ], - "subsets" : [ "http://purl.obolibrary.org/obo/pato#value_slim" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0002-2061-091X" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-09-09T04:50:10Z" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0002318", "lbl" : "superelliptic", @@ -13760,6 +11695,30 @@ "val" : "protein" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/PR_000018263", + "lbl" : "amino acid chain", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.", + "xrefs" : [ "PRO:DAN", "PRO:JSG" ] + }, + "comments" : [ "Category=polymer." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "peptide", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "polypeptide", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/PR_000025796", "lbl" : "integrin alpha", @@ -13836,2941 +11795,6938 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000052", - "lbl" : "characteristic of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/PR_000064867", + "lbl" : "protein-containing molecular entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + "val" : "A molecular entity that minimally consists of a protein.", + "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "protein", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein aggregate", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein complex", + "xrefs" : [ "PRO:DAN" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "protein-containing complex", + "xrefs" : [ "PRO:DAN" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "protein" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000053", - "lbl" : "has characteristic", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000000", + "lbl" : "processual entity", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Inverse of characteristic_of" + "val" : "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", + "xrefs" : [ "span:ProcessualEntity" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "RO:0000053" + "val" : "BFO:0000003" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bearer_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000056", - "lbl" : "participates in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000025", + "lbl" : "tube", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" + "val" : "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical tube" + }, { + "pred" : "hasNarrowSynonym", + "val" : "duct" + } ], "xrefs" : [ { - "val" : "RO:0000056" + "val" : "galen:Tube" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "participates_in" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000057", - "lbl" : "has participant", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000026", + "lbl" : "appendage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" + "val" : "Major subdivision of an organism that protrudes from the body[DOS, CARO].", + "xrefs" : [ "CARO:DOS" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "appendages", + "xrefs" : [ "XAO:0000218" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "extremitaet", + "xrefs" : [ "BTO:0001492" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "extremity" + }, { + "pred" : "hasRelatedSynonym", + "val" : "limbs/digits/tail", + "xrefs" : [ "MP:0000001" ] + } ], "xrefs" : [ { - "val" : "RO:0000057" + "val" : "AEO:0000193" + }, { + "val" : "BILA:0000018" + }, { + "val" : "BTO:0001492" + }, { + "val" : "CARO:0010003" + }, { + "val" : "EFO:0000799" + }, { + "val" : "EHDAA2:0003193" + }, { + "val" : "EMAPA:37283" + }, { + "val" : "EV:0100155" + }, { + "val" : "FBbt:00007000" + }, { + "val" : "HAO:0000144" + }, { + "val" : "MAT:0000023" + }, { + "val" : "MESH:D005121" + }, { + "val" : "MIAA:0000023" + }, { + "val" : "NCIT:C61460" + }, { + "val" : "UMLS:C0598782" + }, { + "val" : "VSAO:0000075" + }, { + "val" : "Wikipedia:Appendage" + }, { + "val" : "XAO:0000218" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_participant" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000080", - "lbl" : "quality of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000055", + "lbl" : "vessel", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" + "val" : "A tubular structure that contains, conveys body fluid, such as blood or lymph.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A quality inheres in its bearer at all times for which the quality exists." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0000086", - "lbl" : "has quality", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000056", + "lbl" : "ureter", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" + "val" : "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.", + "xrefs" : [ "GO:0090189", "Wikipedia:Ureter" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "metanephric duct", + "xrefs" : [ "ISBN:0073040584", "VHOG:0000605" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010254" + }, { + "val" : "BTO:0001409" + }, { + "val" : "CALOHA:TS-1084" + }, { + "val" : "EFO:0000930" + }, { + "val" : "EHDAA2:0002139" + }, { + "val" : "EHDAA:9341" + }, { + "val" : "EMAPA:17950" + }, { + "val" : "EV:0100097" + }, { + "val" : "FMA:9704" + }, { + "val" : "GAID:438" + }, { + "val" : "MA:0000378" + }, { + "val" : "MAT:0000120" + }, { + "val" : "MESH:D014513" + }, { + "val" : "MIAA:0000120" + }, { + "val" : "NCIT:C12416" + }, { + "val" : "SCTID:302511008" + }, { + "val" : "UMLS:C0041951" + }, { + "val" : "VHOG:0000605" + }, { + "val" : "Wikipedia:Ureter" + }, { + "val" : "XAO:0000144" + }, { + "val" : "galen:Ureter" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001000", - "lbl" : "derives from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000057", + "lbl" : "urethra", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening.", + "xrefs" : [ "MGI:anna", "MP:0000537" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "xrefs" : [ { + "val" : "BTO:0001426" + }, { + "val" : "CALOHA:TS-1132" + }, { + "val" : "EFO:0000931" + }, { + "val" : "EMAPA:30901" + }, { + "val" : "EV:0100099" + }, { + "val" : "FMA:19667" + }, { + "val" : "GAID:390" + }, { + "val" : "MA:0000379" + }, { + "val" : "MAT:0000121" + }, { + "val" : "MESH:D014521" + }, { + "val" : "MIAA:0000121" + }, { + "val" : "NCIT:C12417" + }, { + "val" : "SCTID:302513006" + }, { + "val" : "UMLS:C0041967" + }, { + "val" : "VHOG:0001264" + }, { + "val" : "Wikipedia:Urethra" + }, { + "val" : "XAO:0000153" + }, { + "val" : "galen:Urethra" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001001", - "lbl" : "derives into", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "lbl" : "duct", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" + "val" : "A tubular structure that transports secreted or excreted substances.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165", "http://www.siumed.edu/~dking2/intro/glands.htm#ducts" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "anatomical duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine duct" + }, { + "pred" : "hasNarrowSynonym", + "val" : "exocrine gland duct" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "ducts", + "xrefs" : [ "XAO:0004000" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011123" + }, { + "val" : "FBbt:00100314" + }, { + "val" : "FMA:30320" + }, { + "val" : "NCIT:C12948" + }, { + "val" : "SCTID:91726008" + }, { + "val" : "TAO:0005171" + }, { + "val" : "UMLS:C0687028" + }, { + "val" : "Wikipedia:Duct_(anatomy)" + }, { + "val" : "XAO:0004000" + }, { + "val" : "ZFA:0005171" + }, { + "val" : "galen:Duct" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0001015", - "lbl" : "location of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000060", + "lbl" : "anatomical wall", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" + "val" : "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.", + "xrefs" : [ "FMA:82482" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "wall" + }, { + "pred" : "hasExactSynonym", + "val" : "wall of organ", + "xrefs" : [ "FMA:82482" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ wall", + "xrefs" : [ "FMA:82482" ] + } ], + "xrefs" : [ { + "val" : "FMA:82482" + }, { + "val" : "galen:Wall" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. 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See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://wiki.geneontology.org/Located_in" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002000", - "lbl" : "2D boundary of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000062", + "lbl" : "organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" + "val" : "Anatomical structure that performs a specific function or group of functions [WP].", + "xrefs" : [ "Wikipedia:Organ_(anatomy)" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "anatomical unit" + }, { + "pred" : "hasRelatedSynonym", + "val" : "body organ" + }, { + "pred" : "hasRelatedSynonym", + "val" : "element", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BIRNLEX:4" + }, { + "val" : "CARO:0020004" + }, { + "val" : "EFO:0000634" + }, { + "val" : "EMAPA:35949" + }, { + "val" : "ENVO:01000162" + }, { + "val" : "FMA:67498" + }, { + "val" : "MA:0003001" + }, { + "val" : "NCIT:C13018" + }, { + "val" : "SCTID:272625005" + }, { + "val" : "UMLS:C0178784" + }, { + "val" : "WBbt:0003760" + }, { + "val" : "Wikipedia:Organ_(anatomy)" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002002", - "lbl" : "has 2D boundary", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000063", + "lbl" : "organ subunit", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + "val" : "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "organ region with fixed fiat boundary", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "organ segment", + "xrefs" : [ "FMA:86140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "segment of organ", + "xrefs" : [ "FMA:86140" ] + } ], + "xrefs" : [ { + "val" : "FMA:86140" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." + "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002005", - "lbl" : "innervated_by", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002006", - "lbl" : "has synaptic terminal of", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002007", - "lbl" : "bounding layer of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000064", + "lbl" : "organ part", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + "val" : "A multicellular structure that is a part of an organ.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "cardinal organ part", + "xrefs" : [ "FMA:82472" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "regional part of organ", + "xrefs" : [ "BIRNLEX:16" ] + } ], "xrefs" : [ { - "val" : "RO:0002007" + "val" : "AAO:0011124" + }, { + "val" : "BIRNLEX:16" + }, { + "val" : "EFO:0000635" + }, { + "val" : "FMA:82472" + }, { + "val" : "SCTID:113343008" + }, { + "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "bounding_layer_of" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002021", - "lbl" : "occurs across", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000066", + "lbl" : "fully formed stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." + "val" : "The stage of development at which the animal is fully formed, including immaturity and maturity. 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The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO].", + "xrefs" : [ "GO:0001656", "Wikipedia:Metanephros#Metanephros" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "metanephron", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "definite kidney", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "definitive kidney", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "hind kidney", + "xrefs" : [ "BTO:0001543" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metanephric kidney", + "xrefs" : [ "VHOG:0000039" ] + } ], + "xrefs" : [ { + "val" : "BTO:0001543" + }, { + "val" : "EHDAA2:0001137" + }, { + "val" : "EHDAA:3089" + }, { + "val" : "EHDAA:5911" + }, { + "val" : "EMAPA:17373" + }, { + "val" : "EMAPA_RETIRED:17207" + }, { + "val" : "FMA:72172" + }, { + "val" : "NCIT:C34209" + }, { + "val" : "SCTID:308797000" + }, { + "val" : "UMLS:C0231049" + }, { + "val" : "VHOG:0000039" + }, { + "val" : "Wikipedia:Metanephros#Metanephros" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO check developmental relationships" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002113", - "lbl" : "has presynaptic terminal in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000083", + "lbl" : "mesonephric tubule", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." + "val" : "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. 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GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "diverticulum", + "xrefs" : [ "BTO:0001646" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "diverticulum metanephricum", + "xrefs" : [ "Wikipedia:Ureteric_bud" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "gemma ureterica", + "xrefs" : [ "Wikipedia:Ureteric_bud" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metanephric bud", + "xrefs" : [ "BTO:0001646" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "metanephric diverticulum", + "xrefs" : [ "Wikipedia:Metanephros#Metanephros" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "ureteric ampulla" + }, { + "pred" : "hasRelatedSynonym", + "val" : "ureteric diverticulum", + "xrefs" : [ "VHOG:0000541" ] + } ], + "xrefs" : [ { + "val" : "BTO:0001646" + }, { + "val" : "EHDAA2:0002140" + }, { + "val" : "EHDAA:3091" + }, { + "val" : "EHDAA:5917" + }, { + "val" : "EMAPA:17209" + }, { + "val" : "NCIT:C34207" + }, { + "val" : "SCTID:361528000" + }, { + "val" : "UMLS:C1284058" + }, { + "val" : "VHOG:0000541" + }, { + "val" : "Wikipedia:Ureteric_bud" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that part_of some ( that some ( that some Y?)))" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002130", - "lbl" : "has synaptic terminal in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000092", + "lbl" : "post-embryonic stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." + "val" : "Stage succeeding embryo, including mature structure.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "postembryonic stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "post-hatching stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "postembryonic" + } ], + "xrefs" : [ { + "val" : "BilaDO:0000003" + }, { + "val" : "OGES:000010" + }, { + "val" : "OGES:000014" + }, { + "val" : "OGES:000024" + }, { + "val" : "WBls:0000022" + }, { + "val" : "WBls:0000093" + }, { + "val" : "WBls:0000103" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that some Y?)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/344" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002131", - "lbl" : "overlaps", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000104", + "lbl" : "life cycle", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" + "val" : "An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "entire life cycle" + }, { + "pred" : "hasExactSynonym", + "val" : "entire lifespan" + }, { + "pred" : "hasExactSynonym", + "val" : "life" + }, { + "pred" : "hasExactSynonym", + "val" : "lifespan" + } ], "xrefs" : [ { - "val" : "RO:0002131" + "val" : "FBdv:00000000" + }, { + "val" : "HsapDv:0000001" + }, { + "val" : "MmusDv:0000001" + }, { + "val" : "OGES:000011" + }, { + "val" : "ncithesaurus:Life" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "uberon" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "overlaps" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/532" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002132", - "lbl" : "has fasciculating neuron projection", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002134", - "lbl" : "innervates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000105", + "lbl" : "life cycle stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." + "val" : "A spatiotemporal region encompassing some part of the life cycle of an organism.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "developmental stage" + }, { + "pred" : "hasNarrowSynonym", + "val" : "stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000105" + }, { + "val" : "EFO:0000399" + }, { + "val" : "FBdv:00007012" + }, { + "val" : "FMA:24120" + }, { + "val" : "HsapDv:0000000" + }, { + "val" : "MESH:D008018" + }, { + "val" : "MmusDv:0000000" + }, { + "val" : "OlatDv:0000010" + }, { + "val" : "PdumDv:0000090" + }, { + "val" : "WBls:0000002" + }, { + "val" : "XAO:1000000" + }, { + "val" : "ZFS:0000000" + }, { + "val" : "ZFS:0100000" + }, { + "val" : "ncithesaurus:Developmental_Stage" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : " some ( that ( some ( that some Y?)))" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002150", - "lbl" : "continuous with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000106", + "lbl" : "zygote stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + "val" : "A stage at which the organism is a single cell produced by means of sexual reproduction.", + "xrefs" : [ "Wikipedia:Zygote" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "1-cell stage" + }, { + "pred" : "hasExactSynonym", + "val" : "fertilized egg stage", + "xrefs" : [ "BTO:0000854" ] + }, { + "pred" : "hasExactSynonym", + "val" : "one cell stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fertilized egg stage" + }, { + "pred" : "hasRelatedSynonym", + "val" : "one-cell stage", + "xrefs" : [ "VHOG:0000745" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "zygote", + "xrefs" : [ "VHOG:0000745" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "zygotum", + "xrefs" : [ "Wikipedia:Zygote" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000106" + }, { + "val" : "BilaDO:0000005" + }, { + "val" : "EFO:0001322" + }, { + "val" : "EHDAA:27" + }, { + "val" : "FBdv:00005288" + }, { + "val" : "NCIT:C12601" + }, { + "val" : "PdumDv:0000100" + }, { + "val" : "VHOG:0000745" + }, { + "val" : "Wikipedia:Zygote" + }, { + "val" : "XAO:1000001" + }, { + "val" : "ZFS:0000001" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "FMA:85972" + "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002158", - "lbl" : "shares ancestor with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000107", + "lbl" : "cleavage stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + "val" : "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.", + "xrefs" : [ "GO:0040016", "Wikipedia:Cleavage_(embryo)" ] }, - "comments" : [ "VBO calls this homologous_to" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002160", - "lbl" : "only in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000107" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" + "val" : "BilaDO:0000006" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002162", - "lbl" : "in taxon", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." - }, - "comments" : [ "Connects a biological entity to its taxon of origin." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "val" : "EFO:0001290" + }, { + "val" : "FBdv:00000054" + }, { + "val" : "MESH:D002970" + }, { + "val" : "MmusDv:0000004" + }, { + "val" : "OGES:000015" + }, { + "val" : "OGES:000020" + }, { + "val" : "PdumDv:0000200" + }, { + "val" : "Wikipedia:Cleavage_(embryo)" + }, { + "val" : "XAO:1000004" + }, { + "val" : "ZFS:0000046" + } ], "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002163", - "lbl" : "spatially disjoint from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000108", + "lbl" : "blastula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" + "val" : "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.", + "xrefs" : [ "Wikipedia:Blastula" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "xrefs" : [ { + "val" : "BILS:0000108" + }, { + "val" : "BilaDO:0000007" + }, { + "val" : "EFO:0001282" + }, { + "val" : "HsapDv:0000006" + }, { + "val" : "MmusDv:0000007" + }, { + "val" : "OGES:000003" + }, { + "val" : "OGES:000016" + }, { + "val" : "OGES:000021" + }, { + "val" : "WBls:0000005" + }, { + "val" : "Wikipedia:Blastula" + }, { + "val" : "XAO:1000003" + }, { + "val" : "ZFS:0000045" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " + "val" : "consider adding a preceding stage 'morula stage' as part of cleavage" }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", - "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002170", - "lbl" : "connected to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000109", + "lbl" : "gastrula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" + "val" : "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.", + "xrefs" : [ "GO:0007369" ] }, - "basicPropertyValues" : [ { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "blastocystis trilaminaris stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastocyst stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar blastoderm stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar disk stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar germ stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "trilaminar stage", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "BILS:0000109" + }, { + "val" : "BilaDO:0000008" + }, { + "val" : "EFO:0001296" + }, { + "val" : "FBdv:00005317" + }, { + "val" : "HsapDv:0000010" + }, { + "val" : "MmusDv:0000013" + }, { + "val" : "OGES:000004" + }, { + "val" : "OGES:000019" + }, { + "val" : "WBls:0000010" + }, { + "val" : "XAO:1000005" + }, { + "val" : "ZFS:0000047" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present in taxon", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000110", + "lbl" : "neurula stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" + "val" : "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.", + "xrefs" : [ "GO:0001841" ] }, - "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], + "xrefs" : [ { + "val" : "BILS:0000110" + }, { + "val" : "BilaDO:0000009" + }, { + "val" : "HsapDv:0000012" + }, { + "val" : "MmusDv:0000017" + }, { + "val" : "XAO:1000006" + } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", - "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/343" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002176", - "lbl" : "connects", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000111", + "lbl" : "organogenesis stage", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." + "val" : "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.", + "xrefs" : [ "Wikipedia:Organogenesis" ] }, + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "segmentation stage" + } ], + "xrefs" : [ { + "val" : "BILS:0000111" + }, { + "val" : "BilaDO:0000010" + }, { + "val" : "HsapDv:0000015" + }, { + "val" : "MmusDv:0000018" + }, { + "val" : "OGES:000005" + }, { + "val" : "OGES:000032" + }, { + "val" : "Wikipedia:Organogenesis" + } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" + "val" : "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + "val" : "https://github.com/obophenotype/uberon/issues/533" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002177", - "lbl" : "attached to part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002178", - "lbl" : "supplies", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000119", + "lbl" : "cell layer", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + "val" : "Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "layer", + "xrefs" : [ "NCIT:C66831" ] + }, { + "pred" : "hasExactSynonym", + "val" : "layer of cells" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cell sheath" + }, { + "pred" : "hasRelatedSynonym", + "val" : "sheath of cells" + } ], + "xrefs" : [ { + "val" : "NCIT:C66831" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" + "val" : "consider adding to caro" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002179", - "lbl" : "drains", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000154", + "lbl" : "posterior region of body", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." - }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002180", - "lbl" : "has component", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000158", + "lbl" : "membranous layer", + "type" : "CLASS", "meta" : { - "definition" : { - "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002180" + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "membrane" + }, { + "pred" : "hasExactSynonym", + "val" : "membranous organ component", + "xrefs" : [ "FMA:82500" ] } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." + "xrefs" : [ { + "val" : "FMA:30322" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" + "val" : "FMA:82500" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_component" + "val" : "MESH:D008566" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" + "val" : "NCIT:C12749" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002202", - "lbl" : "develops from", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" - }, - "comments" : [ "This is the transitive form of the develops from relation" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002203", - "lbl" : "develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002206", - "lbl" : "expressed in", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002207", - "lbl" : "directly develops from", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000161", + "lbl" : "orifice", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." + "val" : "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].", + "xrefs" : [ "FMA:3724" ] }, - "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "anatomical ostium", + "xrefs" : [ "FMA:3724" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "ostium" + }, { "pred" : "hasExactSynonym", - "val" : "has developmental precursor" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002210", - "lbl" : "directly develops into", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "inverse of directly develops from" - }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002211", - "lbl" : "regulates", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "val" : "anatomical orifice", + "xrefs" : [ "FMA:3724" ] + }, { + "pred" : "hasNarrowSynonym", + "val" : "hilum" + } ], "xrefs" : [ { - "val" : "RO:0002211" + "val" : "FMA:3724" + }, { + "val" : "SCTID:91837002" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002212", - "lbl" : "negatively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000162", + "lbl" : "cloaca", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." + "val" : "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.", + "xrefs" : [ "ISBN:0073040584", "Wikipedia:Cloaca" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "cloacal chamber", + "xrefs" : [ "AAO:0000095" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "vent", + "xrefs" : [ "XAO:0000244" ] + } ], "xrefs" : [ { - "val" : "RO:0002212" + "val" : "AAO:0000095" + }, { + "val" : "GAID:1206" + }, { + "val" : "MESH:D002988" + }, { + "val" : "NCIT:C34127" + }, { + "val" : "SCTID:362857006" + }, { + "val" : "SCTID:370631000" + }, { + "val" : "UMLS:C0008987" + }, { + "val" : "VHOG:0001186" + }, { + "val" : "Wikipedia:Cloaca" + }, { + "val" : "XAO:0000244" + }, { + "val" : "ZFA:0005781" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004050", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "negatively_regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002213", - "lbl" : "positively regulates", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000163", + "lbl" : "embryonic cloaca", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." + "val" : "Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].", + "xrefs" : [ "MP:0010115", "Wikipedia:Cloaca_(embryology)" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "cloaca" + } ], "xrefs" : [ { - "val" : "RO:0002213" + "val" : "EHDAA2:0000256" + }, { + "val" : "EHDAA:4895" + }, { + "val" : "EMAPA:27573" + }, { + "val" : "Wikipedia:Cloaca_(embryology)" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "positively_regulates" + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002215", - "lbl" : "capable of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000164", + "lbl" : "primitive urogenital sinus", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "embryonic tissue", + "xrefs" : [ "FMA:69069" ] }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://en.wikipedia.org/wiki/Tributary" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002379", - "lbl" : "spatially coextensive with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002380", - "lbl" : "branching part of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" - 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." + "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002411", - "lbl" : "causally upstream of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000924", + "lbl" : "ectoderm", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." + "val" : "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.", + "xrefs" : [ "Wikipedia:Ectoderm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic ectoderm", + "xrefs" : [ "VHOG:0000153" ] + } ], "xrefs" : [ { - 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Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002473", - "lbl" : "composed primarily of", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000926", + "lbl" : "mesoderm", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." + "val" : "The middle germ layer of the embryo, between the endoderm and ectoderm.", + "xrefs" : [ "Wikipedia:Mesoderm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "embryonic mesoderm", + "xrefs" : [ "VHOG:0000152" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "entire mesoderm", + "xrefs" : [ "SCTID:362854004", "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "mesodermal mantle" + } ], + "xrefs" : [ { + "val" : "AAO:0000304" + }, { + "val" : "BILA:0000037" + }, { + "val" : "BTO:0000839" + }, { + "val" : "CALOHA:TS-0623" + }, { + "val" : "EFO:0001981" + }, { + "val" : "EHDAA2:0001128" + }, { + "val" : "EHDAA:124" + }, { + "val" : "EHDAA:160" + }, { + "val" : "EHDAA:183" + }, { + "val" : "EMAPA:16083" + }, { + "val" : "EV:0100006" + }, { + "val" : "FBbt:00000126" + }, { + "val" : "FMA:69072" + }, { + "val" : "GAID:522" + }, { + "val" : "MAT:0000174" + }, { + "val" : "MESH:D008648" + }, { + "val" : "MIAA:0000174" + }, { + "val" : "NCIT:C12750" + }, { + "val" : "SCTID:362854004" + }, { + "val" : "TAO:0000041" + }, { + "val" : "UMLS:C0025485" + }, { + "val" : "VHOG:0000152" + }, { + "val" : "Wikipedia:Mesoderm" + }, { + "val" : "XAO:0000050" + }, { + "val" : "ZFA:0000041" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003263" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002479", - "lbl" : "has part that occurs in", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000930", + "lbl" : "stomodeum", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + "val" : "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.", + "xrefs" : [ "Wikipedia:Stomodeum", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/326" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002485", - "lbl" : "receives input from", - "type" : "PROPERTY", - "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "stomodeal-hypophyseal primordium", + "xrefs" : [ "XAO:0000269" ] + }, { + "pred" : "hasExactSynonym", + "val" : "mouth primordium", + "xrefs" : [ "XAO:0000269" ] + }, { + "pred" : "hasExactSynonym", + "val" : "primitive oral cavity", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "stomatodeum", + "xrefs" : [ "Wikipedia:Stomodeum" ] + }, { + "pred" : "hasExactSynonym", + "val" : "stomodaeum" + }, { + "pred" : "hasRelatedSynonym", + "val" : "mouth pit", + "xrefs" : [ "EMAPA:16263" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral ectoderm", + "xrefs" : [ "ZFA:0001290", "ZFIN:ZDB-PUB-100726-23" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "oral pit", + "xrefs" : [ "EMAPA:16263" ] + } ], + "xrefs" : [ { + "val" : "BTO:0004224" + }, { + "val" : "EHDAA2:0001929" + }, { + "val" : "EMAPA:16263" + }, { + "val" : "FBbt:00000439" + }, { + "val" : "FMA:295846" + }, { + "val" : "NCIT:C34306" + }, { + "val" : "TAO:0001290" + }, { + "val" : "TGMA:0000135" + }, { + "val" : "UMLS:C1514977" + }, { + "val" : "Wikipedia:Stomodeum" + }, { + "val" : "XAO:0000269" + }, { + "val" : "ZFA:0001290" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See notes for inverse relation" + "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002486", - "lbl" : "sends output to", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000931", + "lbl" : "proctodeum", + "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.", + "xrefs" : [ "ZFA:0000066", "https://github.com/obophenotype/uberon/issues/685", "https://sourceforge.net/p/fbbtdv/tickets/52" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic proctodaeum" + }, { + "pred" : "hasExactSynonym", + "val" : "proctodaeum" + }, { + "pred" : "hasNarrowSynonym", + "val" : "amnioproctodeal invagination", + "xrefs" : [ "FBbt:00000123" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "anal pit", + "xrefs" : [ "VHOG:0000139" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "anus porus", + "xrefs" : [ "XAO:0001019" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011087" + }, { + "val" : "EHDAA2:0000121" + }, { + "val" : "EMAPA:25038" + }, { + "val" : "FBbt:00000123" + }, { + "val" : "NCIT:C34278" + }, { + "val" : "TAO:0000066" + }, { + "val" : "UMLS:C0231054" + }, { + "val" : "VHOG:0000139" + }, { + "val" : "Wikipedia:Proctodeum" + }, { + "val" : "XAO:0001019" + }, { + "val" : "ZFA:0000066" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." + "val" : "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/685" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002487", - "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002488", - "lbl" : "existence starts during", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002489", - "lbl" : "existence starts with", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002490", - "lbl" : "existence overlaps", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" - }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002491", - "lbl" : "existence starts and ends during", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000948", + "lbl" : "heart", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + "val" : "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.", + "xrefs" : [ "Wikipedia:Heart", "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], + "comments" : [ "Taxon notes:\" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)\" DOI:10.1101/gad.1485706" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "exists during" + "val" : "chambered heart", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "vertebrate heart" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasNarrowSynonym", + "val" : "branchial heart" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardium", + "xrefs" : [ "EMAPA:16105" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010210" + }, { + "val" : "BILA:0000020" + }, { + "val" : "BTO:0000562" + }, { + "val" : "CALOHA:TS-0445" + }, { + "val" : "EFO:0000815" + }, { + "val" : "EHDAA2:0000738" + }, { + "val" : "EHDAA:420" + }, { + "val" : "EMAPA:16105" + }, { + "val" : "EV:0100018" + }, { + "val" : "FMA:7088" + }, { + "val" : "GAID:174" + }, { + "val" : "MA:0000072" + }, { + "val" : "MAT:0000036" + }, { + "val" : "MESH:D006321" + }, { + "val" : "MIAA:0000036" + }, { + "val" : "NCIT:C12727" + }, { + "val" : "SCTID:302509004" + }, { + "val" : "TAO:0000114" + }, { + "val" : "UMLS:C0018787" + }, { + "val" : "VHOG:0000276" + }, { + "val" : "Wikipedia:Heart" + }, { + "val" : "XAO:0000064" + }, { + "val" : "ZFA:0000114" + }, { + "val" : "galen:Heart" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6239" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7227" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002492", - "lbl" : "existence ends during", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000957", + "lbl" : "lamina", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + "val" : "Any thin layer or plate.", + "xrefs" : [ "Wikipedia:Lamina_of_the_vertebral_arch" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "laminar tissue" + } ], + "xrefs" : [ { + "val" : "Wikipedia:Lamina_of_the_vertebral_arch" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - merge with cell layer?" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002493", - "lbl" : "existence ends with", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000958", + "lbl" : "medulla of organ", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." + "val" : "Middle part of an organ, surrounded by the cortex.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002494", - "lbl" : "transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002495", - "lbl" : "immediate transformation of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - } + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "medulla", + "xrefs" : [ "FMA:61108" ] + } ], + "xrefs" : [ { + "val" : "FMA:61108" + }, { + "val" : "galen:Medulla" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] } }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002496", - "lbl" : "existence starts during or after", - "type" : "PROPERTY", + "id" : "http://purl.obolibrary.org/obo/UBERON_0000982", + "lbl" : "skeletal joint", + "type" : "CLASS", "meta" : { "definition" : { - "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + "val" : "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].", + "xrefs" : [ "GO_REF:0000034", "VSAO:0000101", "Wikipedia:Joint", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002497", - "lbl" : "existence ends during or before", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "articulation", + "xrefs" : [ "VSAO:0000101" ] + }, { + "pred" : "hasBroadSynonym", + "val" : "joint", + "xrefs" : [ "FMA:7490", "VSAO:0000101" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "articular joint", + "xrefs" : [ "BTO:0001686" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "joints", + "xrefs" : [ "ZFA:0001596" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000182" + }, { + "val" : "BTO:0001686" + }, { + "val" : "CALOHA:TS-2023" + }, { + "val" : "EFO:0000948" + }, { + "val" : "EMAPA:35456" + }, { + "val" : "FMA:7490" + }, { + "val" : "GAID:102" + }, { + "val" : "MA:0000319" + }, { + "val" : "MAT:0000188" + }, { + "val" : "MESH:D007596" + }, { + "val" : "MIAA:0000188" + }, { + "val" : "NCIT:C13044" + }, { + "val" : "RETIRED_EHDAA2:0003182" + }, { + "val" : "SCTID:302536002" + }, { + "val" : "TAO:0000367" + }, { + "val" : "UMLS:C0022417" + }, { + "val" : "VHOG:0001276" + }, { + "val" : "VSAO:0000101" + }, { + "val" : "Wikipedia:Joint" + }, { + "val" : "XAO:0000171" + }, { + "val" : "ZFA:0001596" + }, { + "val" : "galen:Joint" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0000990", + "lbl" : "reproductive system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Anatomical system that has as its parts the organs concerned with reproduction.", + "xrefs" : [ "Wikipedia:Reproductive_system" ] }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasNarrowSynonym", + "val" : "genital system" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasNarrowSynonym", + "val" : "genitalia" + }, { + "pred" : "hasRelatedSynonym", + "val" : "Geschlechtsorgan", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "animal reproductive system", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "genital tract" + }, { + "pred" : "hasRelatedSynonym", + "val" : "organa genitalia", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "reproductive tissue", + "xrefs" : [ "BTO:0000081" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "reproductive tract" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "systemata genitalia", + "xrefs" : [ "Wikipedia:Reproductive_system" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010258" + }, { + "val" : "BILA:0000103" + }, { + "val" : "BTO:0000081" + }, { + "val" : "CALOHA:TS-1318" + }, { + "val" : "EFO:0000809" + }, { + "val" : "EHDAA2:0001603" + }, { + "val" : "EHDAA:5923" + }, { + "val" : "EMAPA:17381" + }, { + "val" : "EV:0100100" + }, { + "val" : "FBbt:00004857" + }, { + "val" : "FMA:7160" + }, { + "val" : "GAID:363" + }, { + "val" : "HAO:0000374" + }, { + "val" : "HAO:0000895" + }, { + "val" : "MA:0000326" + }, { + "val" : "MIAA:0000305" + }, { + "val" : "NCIT:C12841" + }, { + "val" : "SCTID:278875001" + }, { + "val" : "TAO:0000632" + }, { + "val" : "UMLS:C1261210" + }, { + "val" : "VHOG:0000182" + }, { + "val" : "WBbt:0005747" + }, { + "val" : "Wikipedia:Reproductive_system" + }, { + "val" : "XAO:0000142" + }, { + "val" : "ZFA:0000632" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider splitting genitalia from reproductive system" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2022-06-10T18:22:34Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" + } ] } }, { - 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Examples: vasculature of lung, vasculature of face.", + "xrefs" : [ "ZFA:0005249" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "death" + "pred" : "hasExactSynonym", + "val" : "vascular network", + "xrefs" : [ "FMA:69050" ] } ], "xrefs" : [ { - "val" : "XAO:0000437" + "val" : "BTO:0003718" }, { - "val" : "XtroDO:0000085" + "val" : "FMA:69050" + }, { + "val" : "TAO:0005249" + }, { + "val" : "ZFA:0005249" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "see also: vascular system. 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In metazoans, commences with the zygote stage and ends with the death of the organism.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. 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TODO GCI: relationship: capable_of GO:0030104" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "1-cell stage" - }, { - "pred" : "hasExactSynonym", - "val" : "fertilized egg stage", - "xrefs" : [ "BTO:0000854" ] - }, { - "pred" : "hasExactSynonym", - "val" : "one cell stage" - }, { - "pred" : "hasRelatedSynonym", - "val" : "fertilized egg stage" + "val" : "pronephric kidney", + "xrefs" : [ "XAO:0002000" ] }, { "pred" : "hasRelatedSynonym", - "val" : "one-cell stage", - "xrefs" : [ "VHOG:0000745" ] + "val" : "archinephron", + "xrefs" : [ "BTO:0001541" ] }, { "pred" : "hasRelatedSynonym", - "val" : "zygote", - "xrefs" : [ "VHOG:0000745" ] + "val" : "embryonic kidney", + "xrefs" : [ "BTO:0001541" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "zygotum", - "xrefs" : [ "Wikipedia:Zygote" ] + "val" : "pronephron", + "xrefs" : [ "BTO:0001541" ] } ], "xrefs" : [ { - "val" : "BILS:0000106" + "val" : "AAO:0011089" }, { - "val" : "BilaDO:0000005" + "val" : "BTO:0001541" }, { - "val" : "EFO:0001322" + "val" : "EFO:0000927" }, { - "val" : "EHDAA:27" + "val" : "EHDAA2:0001570" }, { - "val" : "FBdv:00005288" + "val" : "EHDAA:1017" }, { - "val" : "NCIT:C12601" + "val" : "EMAPA:16579" }, { - "val" : "PdumDv:0000100" + "val" : "FMA:72170" }, { - "val" : "VHOG:0000745" + "val" : "MAT:0000117" }, { - "val" : "Wikipedia:Zygote" + "val" : "MIAA:0000117" }, { - "val" : "XAO:1000001" + "val" : "NCIT:C34280" }, { - "val" : "ZFS:0000001" + "val" : "SCTID:308804007" + }, { + "val" : "TAO:0000151" + }, { + "val" : "UMLS:C0231048" + }, { + "val" : "VHOG:0000037" + }, { + "val" : "Wikipedia:Pronephros" + }, { + "val" : "XAO:0002000" + }, { + "val" : "ZFA:0000151" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0005794" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/EMAPA_16033" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000107", - "lbl" : "cleavage stage", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002193", + "lbl" : "hemolymphoid system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. 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It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. 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The blastula follows the morula and precedes the gastrula in the developmental sequence.", - "xrefs" : [ "Wikipedia:Blastula" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blastula embryo", - "xrefs" : [ "BILA:0000059" ] + "pred" : "hasRelatedSynonym", + "val" : "presumptive central nervous system" }, { "pred" : "hasRelatedSynonym", - "val" : "blastosphere", - "xrefs" : [ "Wikipedia:Blastula" ] + "val" : "ventral neurogenic region", + "xrefs" : [ "VHOG:0000150" ] } ], "xrefs" : [ { - "val" : "BILA:0000059" + "val" : "AAO:0011074" }, { - "val" : "BTO:0000128" + "val" : "BILA:0000039" }, { - "val" : "GAID:1294" + "val" : "CALOHA:TS-1212" }, { - "val" : "MESH:D036703" + "val" : "EHDAA2:0001248" }, { - "val" : "OGEM:000006" + "val" : "EHDAA:1498" }, { - "val" : "Wikipedia:Blastula" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" + "val" : "EHDAA:255" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007011" + "val" : "EMAPA:16073" + }, { + "val" : "EV:0100004" + }, { + "val" : "FBbt:00001057" + }, { + "val" : "FMA:87657" + }, { + "val" : "MAT:0000176" + }, { + "val" : "MIAA:0000176" + }, { + "val" : "NCIT:C34228" + }, { + "val" : "TAO:0001120" + }, { + "val" : "UMLS:C1518271" + }, { + "val" : "VHOG:0000150" }, { + "val" : "Wikipedia:Neuroectoderm" + }, { + "val" : "XAO:0000042" + }, { + "val" : "ZFA:0001120" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000353", - "lbl" : "parenchyma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002355", + "lbl" : "pelvic region of trunk", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues.", - "xrefs" : [ "Wikipedia:Parenchyma" ] + "val" : "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.", + "xrefs" : [ "Wikipedia:Pelvis", "http://orcid.org/0000-0002-6601-2165", "https://github.com/obophenotype/uberon/issues/720" ] }, - "xrefs" : [ { - "val" : "EHDAA:3015" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "lesser pelvis", + "xrefs" : [ "FMA:9578" ] }, { - "val" : "EHDAA:3905" + "pred" : "hasExactSynonym", + "val" : "pelvic region" }, { - "val" : "EHDAA:3999" + "pred" : "hasExactSynonym", + "val" : "pelvis", + "xrefs" : [ "FMA:9578", "MA:0000030" ] }, { - "val" : "EHDAA:4005" + "pred" : "hasExactSynonym", + "val" : "pelvis region" }, { - "val" : "EHDAA:6899" + "pred" : "hasExactSynonym", + "val" : "true pelvis", + "xrefs" : [ "FMA:9578" ] + } ], + "xrefs" : [ { + "val" : "BTO:0001006" }, { - "val" : "EHDAA:6903" + "val" : "CALOHA:TS-2227" }, { - "val" : "EHDAA:6994" + "val" : "EFO:0002805" }, { - "val" : "EHDAA:8086" + "val" : "EMAPA:35931" }, { - "val" : "EHDAA:9182" + "val" : "EV:0100012" }, { - "val" : "EHDAA:9190" + "val" : "FMA:9578" }, { - "val" : "EHDAA:9196" + "val" : "GAID:87" }, { - "val" : "EHDAA:9202" + "val" : "MA:0000030" }, { - "val" : "FMA:45732" + "val" : "MESH:D010388" }, { - "val" : "NCIT:C74601" + "val" : "NCIT:C12767" }, { - "val" : "UMLS:C0933845" + "val" : "SCTID:229765004" }, { - "val" : "Wikipedia:Parenchyma" + "val" : "UMLS:C0030797" + }, { + "val" : "Wikipedia:Pelvis" + }, { + "val" : "galen:Pelvis" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -18793,86 +20795,65 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000362", - "lbl" : "renal medulla", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002384", + "lbl" : "connective tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The inner portion of the kidney consisting of the renal pyramids.", - "xrefs" : [ "ISBN:0-683-40008-8", "MGI:smb", "MP:0003014" ] + "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000017", "http://dx.plos.org/10.1371/journal.pone.0051070", "https://github.com/obophenotype/uberon/issues/23" ] }, - "comments" : [ "Note that 'renal medulla' is not synonymous with 'medullary region of kidney'. The former is composed of kidney pyramids only, while the latter covers kidney pyramids and renal columns, which are histologically different." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "kidney medulla", - "xrefs" : [ "OBOL:automatic" ] + "val" : "portion of connective tissue", + "xrefs" : [ "FMA:9640" ] }, { "pred" : "hasExactSynonym", - "val" : "medulla of kidney", - "xrefs" : [ "OBOL:automatic" ] + "val" : "textus connectivus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "medulla renalis", - "xrefs" : [ "FMA:74268", "FMA:TA" ] + "pred" : "hasRelatedSynonym", + "val" : "Bindegewebe", + "xrefs" : [ "BTO:0000421" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000098" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "pyramides renales", - "xrefs" : [ "FMA:74268", "FMA:TA" ] + "val" : "BTO:0000421" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal medullae", - "xrefs" : [ "FMA:86327" ] + "val" : "CALOHA:TS-2009" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal medullae set", - "xrefs" : [ "FMA:86327" ] + "val" : "EFO:0000952" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal pyramids", - "xrefs" : [ "FMA:74268" ] + "val" : "EMAPA:35251" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "renal pyramids set", - "xrefs" : [ "FMA:74268" ] + "val" : "FMA:9640" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "medullary pyramids", - "xrefs" : [ "FMA:74268" ] + "val" : "GAID:100" }, { - "pred" : "hasRelatedSynonym", - "val" : "renal marrow", - "xrefs" : [ "BTO:0001167" ] - } ], - "xrefs" : [ { - "val" : "BTO:0001167" + "val" : "MA:0000011" }, { - "val" : "CALOHA:TS-1157" + "val" : "MAT:0000301" }, { - "val" : "EMAPA:19279" + "val" : "MESH:D003238" }, { - "val" : "GAID:425" + "val" : "MIAA:0000301" }, { - "val" : "MA:0000373" + "val" : "NCIT:C12374" }, { - "val" : "MESH:D007679" + "val" : "SCTID:361919005" }, { - "val" : "NCIT:C12740" + "val" : "TAO:0001641" }, { - "val" : "SCTID:30737000" + "val" : "UMLS:C0009780" }, { - "val" : "UMLS:C0022664" + "val" : "VSAO:0000017" }, { - "val" : "Wikipedia:Renal_medulla" + "val" : "XAO:0001017" }, { - "val" : "galen:MedullaOfKidney" + "val" : "ZFA:0001632" + }, { + "val" : "galen:ConnectiveTissue" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -18880,1173 +20861,1101 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "lbl" : "musculature of body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", + "lbl" : "muscle tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].", - "xrefs" : [ "VSAO:0000033" ] + "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", + "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "pred" : "hasExactSynonym", - "val" : "muscle system" - }, { - "pred" : "hasExactSynonym", - "val" : "muscle system of body" - }, { - "pred" : "hasExactSynonym", - "val" : "muscular system", - "xrefs" : [ "FMA:72954" ] - }, { - "pred" : "hasExactSynonym", - "val" : "musculature system", - "xrefs" : [ "BILA:0000088" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all muscles", - "xrefs" : [ "FMA:72954" ] + "val" : "muscular tissue" }, { "pred" : "hasExactSynonym", - "val" : "set of muscles of body", - "xrefs" : [ "FMA:72954" ] + "val" : "portion of muscle tissue", + "xrefs" : [ "FMA:9641" ] }, { "pred" : "hasExactSynonym", - "val" : "vertebrate muscular system", - "xrefs" : [ "BTO:0001369" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "muskelsystem", - "xrefs" : [ "BTO:0001485" ] + "val" : "textus muscularis" } ], "xrefs" : [ { - "val" : "AAO:0000307" - }, { - "val" : "BILA:0000088" + "val" : "AAO:0000306" }, { - "val" : "BTO:0001369" + "val" : "AEO:0000122" }, { - "val" : "BTO:0001485" + "val" : "CALOHA:TS-0642" }, { - "val" : "EFO:0000801" + "val" : "EHDAA2:0003122" }, { - "val" : "FMA:72954" + "val" : "EMAPA:32715" }, { - "val" : "MA:0002888" + "val" : "FMA:9641" }, { - "val" : "MAT:0000025" + "val" : "MA:0002437" }, { - "val" : "MIAA:0000025" + "val" : "MESH:D009132" }, { - "val" : "VSAO:0000033" + "val" : "NCIT:C12435" }, { - "val" : "XAO:0004042" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" + "val" : "SCTID:91727004" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "val" : "UMLS:C2328219" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "Wikipedia:Muscle_tissue" }, { + "val" : "galen:MuscleTissue" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000463", - "lbl" : "organism substance", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", + "lbl" : "hematopoietic system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "Anatomical system that is involved in the production of hematopoietic cells.", + "xrefs" : [ "Wikipedia:Haematopoiesis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "body fluid or substance", - "xrefs" : [ "MA:0002450" ] + "val" : "haematological system" }, { "pred" : "hasExactSynonym", - "val" : "body substance", - "xrefs" : [ "FMA:9669" ] + "val" : "haemopoietic system" }, { "pred" : "hasExactSynonym", - "val" : "organism substance", - "xrefs" : [ "CARO:0000004" ] + "val" : "organa haemopoietica" }, { - "pred" : "hasExactSynonym", - "val" : "portion of body substance", - "xrefs" : [ "FMA:9669" ] + "pred" : "hasRelatedSynonym", + "val" : "Blutbildungssystem", + "xrefs" : [ "BTO:0000570" ] }, { - "pred" : "hasExactSynonym", - "val" : "portion of organism substance", - "xrefs" : [ "ZFA:0001487" ] + "pred" : "hasRelatedSynonym", + "val" : "haematopoietic system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hematological system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hematolymphoid system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "hemopoietic system" } ], "xrefs" : [ { - "val" : "AAO:0010839" + "val" : "AAO:0011002" + }, { + "val" : "BTO:0000570" }, { - "val" : "AEO:0000004" + "val" : "CALOHA:TS-0449" }, { - "val" : "BILA:0000004" + "val" : "EFO:0000798" }, { - "val" : "CALOHA:TS-2101" + "val" : "EMAPA:35402" }, { - "val" : "CARO:0000004" + "val" : "EV:0100045" }, { - "val" : "EHDAA2:0003004" + "val" : "FMA:9667" }, { - "val" : "EMAPA:35178" + "val" : "GAID:1008" }, { - "val" : "FBbt:00007019" + "val" : "MA:0002434" }, { - "val" : "FMA:9669" + "val" : "MAT:0000022" }, { - "val" : "HAO:0000004" + "val" : "MESH:D006413" }, { - "val" : "MA:0002450" + "val" : "MIAA:0000022" }, { - "val" : "NCIT:C13236" + "val" : "NCIT:C12909" }, { - "val" : "SPD:0000008" + "val" : "SCTID:362587009" }, { - "val" : "TAO:0001487" + "val" : "TAO:0005023" }, { - "val" : "TGMA:0001824" + "val" : "UMLS:C0018957" }, { - "val" : "VHOG:0001726" + "val" : "VHOG:0001624" }, { - "val" : "XAO:0004001" + "val" : "Wikipedia:Haematopoiesis" }, { - "val" : "ZFA:0001487" + "val" : "XAO:0000122" }, { - "val" : "galen:BodySubstance" + "val" : "ZFA:0005023" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000464", - "lbl" : "anatomical space", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002417", + "lbl" : "abdominal segment of trunk", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "The abdominal segment of the torso.", + "xrefs" : [ "Wikipedia:Lumbar" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "lumen" + "pred" : "hasRelatedSynonym", + "val" : "abdomen/pelvis/perineum", + "xrefs" : [ "MA:0000021" ] }, { - "pred" : "hasBroadSynonym", - "val" : "space" + "pred" : "hasRelatedSynonym", + "val" : "lower body", + "xrefs" : [ "MA:0000021" ] }, { - "pred" : "hasExactSynonym", - "val" : "lumen space" + "pred" : "hasRelatedSynonym", + "val" : "lower trunk", + "xrefs" : [ "FMA:259211" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "anatomical spaces", - "xrefs" : [ "ZFA:0001643" ] + "val" : "lumbar region", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { - "val" : "AAO:0010110" - }, { - "val" : "AEO:0000005" - }, { - "val" : "BILA:0000005" - }, { - "val" : "CARO:0000005" - }, { - "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" - }, { - "val" : "FMA:5897" - }, { - "val" : "HAO:0000005" - }, { - "val" : "NCIT:C94478" - }, { - "val" : "TAO:0001668" - }, { - "val" : "TGMA:0001825" + "val" : "EMAPA:35104" }, { - "val" : "UMLS:C0524461" + "val" : "FMA:259211" }, { - "val" : "VHOG:0001728" + "val" : "MA:0000021" }, { - "val" : "XAO:0003190" + "val" : "SCTID:362875007" }, { - "val" : "ZFA:0001643" + "val" : "Wikipedia:Lumbar" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000465", - "lbl" : "material anatomical entity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", + "lbl" : "epiblast (generic)", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical entity that has mass.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", + "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "AAO:0010264" - }, { - "val" : "AEO:0000006" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "epiblast", + "xrefs" : [ "VHOG:0000243" ] }, { - "val" : "BILA:0000006" + "pred" : "hasRelatedSynonym", + "val" : "blastocyst" }, { - "val" : "CARO:0000006" + "pred" : "hasRelatedSynonym", + "val" : "ectoblast", + "xrefs" : [ "MP:0003886" ] }, { - "val" : "EHDAA2:0003006" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "epiblastus", + "xrefs" : [ "Wikipedia:Epiblast" ] }, { - "val" : "FBbt:00007016" + "pred" : "hasRelatedSynonym", + "val" : "primitive ectoderm", + "xrefs" : [ "VHOG:0000243" ] + } ], + "xrefs" : [ { + "val" : "BTO:0004593" }, { - "val" : "FMA:67165" + "val" : "FMA:296704" }, { - "val" : "HAO:0000006" + "val" : "MAT:0000067" }, { - "val" : "TAO:0001836" + "val" : "MIAA:0000067" }, { - "val" : "TGMA:0001826" + "val" : "VHOG:0000243" }, { - "val" : "VHOG:0001721" + "val" : "Wikipedia:Epiblast" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. 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Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", + "xrefs" : [ "FMA:67552" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "immaterial physical anatomical entity", - "xrefs" : [ "FMA:67112" ] + "pred" : "hasBroadSynonym", + "val" : "cavity" } ], "xrefs" : [ { - "val" : "AAO:0010265" - }, { - "val" : "AEO:0000007" - }, { - "val" : "BILA:0000007" - }, { - "val" : "CARO:0000007" - }, { - "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" + "val" : "BIRNLEX:1011" }, { - "val" : "FMA:67112" + "val" : "EMAPA:37442" }, { - "val" : "HAO:0000007" + "val" : "FMA:67552" }, { - "val" : "TAO:0001835" + "val" : "MA:0002447" }, { - "val" : "TGMA:0001827" + "val" : "NCIT:C34007" }, { - 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Examples: pulmonary alveolar epithelium, endothelium.[FMA].", - "xrefs" : [ "FMA:45565", "Wikipedia:Simple_squamous_epithelium", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "An organ involved in reproduction.", + "xrefs" : [ "UBERON:xp" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "epithelium simplex squamosum" + "val" : "genital organ" + }, { + "pred" : "hasExactSynonym", + "val" : "reproductive system organ" + }, { + "pred" : "hasExactSynonym", + "val" : "sex organ" }, { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "simple squamous epithelia", - "xrefs" : [ "ZFA:0001498" ] + "val" : "genitalia" } ], "xrefs" : [ { - "val" : "AAO:0010066" - }, { - "val" : "AEO:0000070" - }, { - "val" : "BILA:0000070" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000070" - }, { - "val" : "EHDAA2:0003070" - }, { - "val" : "FMA:45565" + "val" : "EMAPA:37731" }, { - "val" : "HAO:0000070" + "val" : "MA:0001752" }, { - "val" : "NCIT:C13178" + "val" : "MESH:D005835" }, { - "val" : "TAO:0001498" + "val" : "NCIT:C25177" }, { - "val" : "UMLS:C0836133" + "val" : "SCTID:128181006" }, { - "val" : "Wikipedia:Simple_squamous_epithelium" + "val" : "TGMA:0000591" }, { - "val" : "XAO:0004010" + "val" : "UMLS:C0017420" }, { - "val" : "ZFA:0001498" + "val" : "WBbt:0008422" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000489", - "lbl" : "cavitated compound organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003220", + "lbl" : "metanephric mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Compound organ that contains one or more macroscopic anatomical spaces.", - "xrefs" : [ "http://orcid.org/0000-0001-9114-8737" ] + "val" : "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].", + "xrefs" : [ "GO:0072075", "Wikipedia:Metanephric_blastema" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "comments" : [ "Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 \"Developmental Biology\"]" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "cavitated organ", - "xrefs" : [ "FMA:55671" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "cavitated compound organs", - "xrefs" : [ "ZFA:0001490" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010016" - }, { - "val" : "AEO:0000072" + "val" : "metanephric blastema", + "xrefs" : [ "Wikipedia:Metanephric_blastema" ] }, { - "val" : "BILA:0000072" + "pred" : "hasExactSynonym", + "val" : "metanephric mesoderm", + "xrefs" : [ "Wikipedia:Metanephric_blastema" ] }, { - "val" : "CARO:0000072" + "pred" : "hasExactSynonym", + "val" : "metanephrogenic mesenchyme", + "xrefs" : [ "EHDAA:5021" ] }, { - "val" : "EHDAA2:0003072" + "pred" : "hasExactSynonym", + "val" : "metanephros associated mesenchyme", + "xrefs" : [ "RETIRED_EHDAA2:0001139" ] + } ], + "xrefs" : [ { + "val" : "EHDAA2:0004062" }, { - "val" : "FMA:55671" + "val" : "EHDAA:4041" }, { - "val" : "HAO:0000072" + "val" : "EHDAA:5021" }, { - "val" : "TAO:0001490" + "val" : "EHDAA:5915" }, { - "val" : "TGMA:0001857" + "val" : "EMAPA:17375" }, { - "val" : "VHOG:0001730" + "val" : "SCTID:361529008" }, { - "val" : "XAO:0003165" + "val" : "VHOG:0000540" }, { - "val" : "ZFA:0001490" + "val" : "Wikipedia:Metanephric_blastema" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -20054,97 +21963,98 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000490", - "lbl" : "unilaminar epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003479", + "lbl" : "thoracic cavity vein", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA].", - "xrefs" : [ "FMA:45561", "http://orcid.org/0000-0001-9114-8737" ] + "val" : "A vein that is part of a thoracic cavity [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "simple epithelium", - "xrefs" : [ "FMA:45561" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "unilaminar epithelia", - "xrefs" : [ "ZFA:0001495" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010062" - }, { - "val" : "AEO:0000073" - }, { - "val" : "BILA:0000073" - }, { - "val" : "BTO:0002073" - }, { - "val" : "CARO:0000073" + "val" : "cavity of chest vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "EHDAA2:0003073" + "pred" : "hasExactSynonym", + "val" : "cavity of thorax vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "FMA:45561" + "pred" : "hasExactSynonym", + "val" : "chest cavity vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "HAO:0000073" + "pred" : "hasExactSynonym", + "val" : "pectoral cavity vein", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "NCIT:C33554" + "pred" : "hasExactSynonym", + "val" : "vein of cavity of chest", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "SCTID:309043004" + "pred" : "hasExactSynonym", + "val" : "vein of cavity of thorax", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "TAO:0001495" + "pred" : "hasExactSynonym", + "val" : "vein of chest cavity", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "UMLS:C0682574" + "pred" : "hasExactSynonym", + "val" : "vein of pectoral cavity", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "XAO:0004007" + "pred" : "hasExactSynonym", + "val" : "vein of thoracic cavity", + "xrefs" : [ "OBOL:automatic" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37242" }, { - "val" : "ZFA:0001495" + "val" : "MA:0001903" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000915", - "lbl" : "thoracic segment of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003497", + "lbl" : "abdomen blood vessel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Subdivision of trunk that lies between the head and the abdomen.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A blood vessel that is part of an abdomen [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "thorax", - "xrefs" : [ "MA:0000022" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "anterior subdivision of trunk" - }, { - "pred" : "hasRelatedSynonym", - "val" : "upper body" - }, { - "pred" : "hasRelatedSynonym", - "val" : "upper trunk", - "xrefs" : [ "FMA:259209" ] + "val" : "blood vessel of abdomen", + "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "EMAPA:35862" - }, { - "val" : "FMA:259209" - }, { - "val" : "MA:0000022" - }, { - "val" : "SCTID:302551006" + "val" : "MA:0000518" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0003509", + "lbl" : "arterial blood vessel", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "only in MA - supertype of artery, arteriole, aorta." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "xrefs" : [ { + "val" : "EMAPA:35144" }, { - "val" : "Wikipedia:Thorax" + "val" : "MA:0000061" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -20152,220 +22062,246 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000916", - "lbl" : "abdomen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0003513", + "lbl" : "trunk blood vessel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A blood vessel that is part of a trunk [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "abdominopelvic region", - "xrefs" : [ "FMA:9577" ] + "val" : "blood vessel of torso", + "xrefs" : [ "OBOL:automatic" ] }, { "pred" : "hasExactSynonym", - "val" : "abdominopelvis", - "xrefs" : [ "FMA:9577" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "adult abdomen" - }, { - "pred" : "hasRelatedSynonym", - "val" : "belly" + "val" : "blood vessel of trunk", + "xrefs" : [ "OBOL:automatic" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "celiac region" + "pred" : "hasExactSynonym", + "val" : "torso blood vessel", + "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "BTO:0000020" - }, { - "val" : "CALOHA:TS-0001" - }, { - "val" : "EFO:0000968" - }, { - "val" : "EMAPA:35102" - }, { - "val" : "EV:0100011" - }, { - "val" : "FMA:9577" - }, { - "val" : "GAID:16" - }, { - "val" : "MA:0000029" - }, { - "val" : "MAT:0000298" - }, { - "val" : "MESH:D000005" - }, { - "val" : "MIAA:0000298" - }, { - "val" : "SCTID:302553009" - }, { - "val" : "Wikipedia:Abdomen" + "val" : "EMAPA:37237" }, { - "val" : "galen:Abdomen" + "val" : "MA:0000511" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Vertebrate specific. 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"id" : "http://purl.obolibrary.org/obo/UBERON_0000982", - "lbl" : "skeletal joint", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004122", + "lbl" : "genitourinary system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].", - "xrefs" : [ "GO_REF:0000034", "VSAO:0000101", "Wikipedia:Joint", "http://dx.plos.org/10.1371/journal.pone.0051070" ] + "val" : "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.", + "xrefs" : [ "VHOG:0000286" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "articulation", - "xrefs" : [ "VSAO:0000101" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "joint", - "xrefs" : [ "FMA:7490", "VSAO:0000101" ] + "pred" : "hasExactSynonym", + "val" : "urogenital system" }, { "pred" : "hasRelatedSynonym", - "val" : "articular joint", - "xrefs" : [ "BTO:0001686" ] + "val" : "GU tract" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "joints", - "xrefs" : [ "ZFA:0001596" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000182" - }, { - "val" : "BTO:0001686" - }, { - "val" : "CALOHA:TS-2023" + "val" : "UG tract" }, { - "val" : "EFO:0000948" + "pred" : "hasRelatedSynonym", + "val" : "Urogenitalsystem", + "xrefs" : [ "BTO:0003091" ] }, { - "val" : "EMAPA:35456" + "pred" : "hasRelatedSynonym", + "val" : "genito-urinary system", + "xrefs" : [ "FMA:280610" ] }, { - "val" : "FMA:7490" + "pred" : "hasRelatedSynonym", + "val" : "genitourinary tract" }, { - "val" : "GAID:102" + "pred" : "hasRelatedSynonym", + "val" : "urogenital tract", + "xrefs" : [ "BTO:0003091" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000624" }, { - "val" : "MA:0000319" + "val" : "BILA:0000122" }, { - "val" : "MAT:0000188" + "val" : "BTO:0003091" }, { - "val" : "MESH:D007596" + "val" : "EFO:0003864" }, { - "val" : "MIAA:0000188" + "val" : "EHDAA:1013" }, { - "val" : "NCIT:C13044" + "val" : "EMAPA:16367" }, { - "val" : "RETIRED_EHDAA2:0003182" + "val" : "EV:0100094" }, { - "val" : "SCTID:302536002" + "val" : "FMA:280610" }, { - "val" : "TAO:0000367" + "val" : "GAID:362" }, { - "val" : "UMLS:C0022417" + "val" : "MESH:D014566" }, { - "val" : "VHOG:0001276" + "val" : "NCIT:C12810" }, { - "val" : "VSAO:0000101" + "val" : "SCTID:278861008" }, { - "val" : "Wikipedia:Joint" + "val" : "UMLS:C0042066" }, { - "val" : "XAO:0000171" + "val" : "VHOG:0000286" }, { - "val" : "ZFA:0001596" + "val" : "XAO:0000140" }, { - "val" : "galen:Joint" + "val" : "galen:GenitoUrinarySystem" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -20973,665 +22722,370 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000990", - "lbl" : "reproductive system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004134", + "lbl" : "proximal tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that has as its parts the organs concerned with reproduction.", - "xrefs" : [ "Wikipedia:Reproductive_system" ] + "val" : "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].", + "xrefs" : [ "GO:0072014" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "genital system" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasNarrowSynonym", - "val" : "genitalia" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Geschlechtsorgan", - "xrefs" : [ "BTO:0000081" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "animal reproductive system", - "xrefs" : [ "BTO:0000081" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "genital tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "organa genitalia", - "xrefs" : [ "BTO:0000081" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "reproductive tissue", - "xrefs" : [ "BTO:0000081" ] + "pred" : "hasExactSynonym", + "val" : "kidney proximal tubule", + "xrefs" : [ "MA:0002611" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "reproductive tract" + "pred" : "hasExactSynonym", + "val" : "proximal kidney tubule", + "xrefs" : [ "MESH:A05.810.453.736.560.570" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "systemata genitalia", - "xrefs" : [ "Wikipedia:Reproductive_system" ] + "pred" : "hasExactSynonym", + "val" : "renal proximal tubule" } ], "xrefs" : [ { - "val" : "AAO:0010258" - }, { - "val" : "BILA:0000103" - }, { - "val" : "BTO:0000081" - }, { - "val" : "CALOHA:TS-1318" - }, { - "val" : "EFO:0000809" - }, { - "val" : "EHDAA2:0001603" - }, { - "val" : "EHDAA:5923" - }, { - "val" : "EMAPA:17381" - }, { - "val" : "EV:0100100" - }, { - "val" : "FBbt:00004857" - }, { - "val" : "FMA:7160" - }, { - "val" : "GAID:363" - }, { - "val" : "HAO:0000374" - }, { - "val" : "HAO:0000895" - }, { - "val" : "MA:0000326" - }, { - "val" : "MIAA:0000305" - }, { - "val" : "NCIT:C12841" - }, { - "val" : "SCTID:278875001" - }, { - "val" : "TAO:0000632" - }, { - "val" : "UMLS:C1261210" - }, { - "val" : "VHOG:0000182" + "val" : "BTO:0001498" }, { - "val" : "WBbt:0005747" + "val" : "CALOHA:TS-0509" }, { - "val" : "Wikipedia:Reproductive_system" + "val" : "EMAPA:28281" }, { - "val" : "XAO:0000142" + "val" : "MA:0002611" }, { - "val" : "ZFA:0000632" + "val" : "MESH:D007687" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider splitting genitalia from reproductive system" + "val" : "TODO - ensure definition works across species." }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2022-06-10T18:22:34Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0000991", - "lbl" : "gonad", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004135", + "lbl" : "distal tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Reproductive organ that produces and releases eggs (ovary) or sperm (testis).", - "xrefs" : [ "ISBN:0140512888", "Wikipedia:Gonad", "ZFA:0000413", "ZFIN:curator" ] + "val" : "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments.", + "xrefs" : [ "GO:0072017" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "gonada" + "val" : "kidney distal tubule", + "xrefs" : [ "MA:0002633" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "gonads", - "xrefs" : [ "ZFA:0000413" ] + "pred" : "hasExactSynonym", + "val" : "renal distal tubule" } ], "xrefs" : [ { - "val" : "AAO:0000213" - }, { - "val" : "BILA:0000123" - }, { - "val" : "BSA:0000079" - }, { - "val" : "BTO:0000534" - }, { - "val" : "EMAPA:17383" - }, { - "val" : "FMA:18250" - }, { - "val" : "GAID:368" - }, { - "val" : "HAO:0000379" - }, { - "val" : "MA:0002420" - }, { - "val" : "MESH:D006066" - }, { - "val" : "NCIT:C12725" - }, { - "val" : "SCTID:304623008" - }, { - "val" : "TAO:0000413" - }, { - "val" : "UMLS:C0018067" + "val" : "BTO:0000482" }, { - "val" : "VHOG:0000397" + "val" : "CALOHA:TS-0504" }, { - "val" : "WBbt:0005175" + "val" : "EMAPA:28387" }, { - "val" : "Wikipedia:Gonad" + "val" : "MA:0002633" }, { - "val" : "XAO:0003146" + "val" : "MESH:D007686" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004136", + "lbl" : "intermediate tubule", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules.", + "xrefs" : [ "GO:0072018" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "renal intermediate tubule" }, { - "val" : "ZFA:0000413" + "pred" : "hasExactSynonym", + "val" : "tubulus attenuatus", + "xrefs" : [ "FMA:17718" ] + } ], + "xrefs" : [ { + "val" : "FMA:17718" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check for applicability across species" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001007", - "lbl" : "digestive system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", + "lbl" : "cardiogenic plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.", - "xrefs" : [ "FB:gg", "NLM:alimentary+system", "Wikipedia:Digestive_system" ] + "val" : "The first recognizable structure derived from the heart field.", + "xrefs" : [ "GO:0003142" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system" + "pred" : "hasExactSynonym", + "val" : "myocardial plate", + "xrefs" : [ "EHDAA2:0000215" ] }, { "pred" : "hasRelatedSynonym", - "val" : "alimentary tract" + "val" : "cardiac crescent", + "xrefs" : [ "EMAPA:16106" ] }, { "pred" : "hasRelatedSynonym", - "val" : "gastrointestinal system" + "val" : "cardiogenic crescent", + "xrefs" : [ "GO:0003142" ] }, { "pred" : "hasRelatedSynonym", - "val" : "gut" + "val" : "heart rudiment" } ], "xrefs" : [ { - "val" : "AAO:0000129" - }, { - "val" : "BILA:0000082" - }, { - "val" : "BTO:0000058" - }, { - "val" : "CALOHA:TS-1293" - }, { - "val" : "EFO:0000793" - }, { - "val" : "FBbt:00005055" - }, { - "val" : "FMA:7152" - }, { - "val" : "GAID:278" - }, { - "val" : "MA:0002431" - }, { - "val" : "MAT:0000018" - }, { - "val" : "MESH:D004064" - }, { - "val" : "MIAA:0000018" - }, { - "val" : "SCTID:278859004" - }, { - "val" : "TADS:0000170" - }, { - "val" : "TAO:0000339" - }, { - "val" : "WBbt:0005748" - }, { - "val" : "Wikipedia:Digestive_system" - }, { - "val" : "XAO:0000125" - }, { - "val" : "ZFA:0000339" + "val" : "EHDAA2:0000215" }, { - "val" : "galen:DigestiveSystem" + "val" : "EMAPA:16106" }, { - "val" : "ncithesaurus:Digestive_System" + "val" : "VHOG:0000975" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001008", - "lbl" : "renal system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "lbl" : "primary heart field", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.", - "xrefs" : [ "DOI:10.1371/journal.pone.0099864", "GO:0072001" ] + "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", + "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] }, - "comments" : [ "EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "excretory system" - }, { - "pred" : "hasExactSynonym", - "val" : "systema urinaria", - "xrefs" : [ "FMA:7159" ] - }, { "pred" : "hasExactSynonym", - "val" : "systema urinarium", - "xrefs" : [ "BTO:0003092" ] + "val" : "first heart field", + "xrefs" : [ "XAO:0004185" ] }, { "pred" : "hasExactSynonym", - "val" : "urinary system" + "val" : "primary heart field", + "xrefs" : [ "PMID:17276708", "XAO:0004185" ] }, { - "pred" : "hasExactSynonym", - "val" : "urinary tract" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "FHF", + "xrefs" : [ "XAO:0004185" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasRelatedSynonym", - "val" : "renal or urinary system", - "xrefs" : [ "EHDAA:5901" ] + "val" : "PHF", + "xrefs" : [ "XAO:0004185" ] }, { "pred" : "hasRelatedSynonym", - "val" : "renal/urinary system" + "val" : "heart field", + "xrefs" : [ "XAO:0004185" ] } ], "xrefs" : [ { - "val" : "AAO:0010257" - }, { - "val" : "BILA:0000015" - }, { - "val" : "BTO:0001244" - }, { - "val" : "BTO:0003092" - }, { - "val" : "CALOHA:TS-1323" - }, { - "val" : "EFO:0000803" - }, { - "val" : "EHDAA2:0001601" - }, { - "val" : "EHDAA:5901" - }, { - "val" : "EMAPA:17366" - }, { - "val" : "EV:0100095" - }, { - "val" : "FBbt:00005056" - }, { - "val" : "FMA:7159" - }, { - "val" : "GAID:391" - }, { - "val" : "MA:0000325" - }, { - "val" : "MAT:0000027" - }, { - "val" : "MESH:D014551" - }, { - "val" : "MIAA:0000027" - }, { - "val" : "NCIT:C12413" - }, { - "val" : "SCTID:362204003" - }, { - "val" : "TADS:0000162" + "val" : "XAO:0004185" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", + "lbl" : "heart tube", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An epithelial tube that will give rise to the mature heart.", + "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "embryonic heart tube", + "xrefs" : [ "GO:0003143" ] }, { - "val" : "TAO:0000163" + "pred" : "hasExactSynonym", + "val" : "endocardial heart tube", + "xrefs" : [ "MP:0012700" ] }, { - "val" : "UMLS:C1508753" + "pred" : "hasExactSynonym", + "val" : "endocardial tube", + "xrefs" : [ "XAO:0000337" ] + } ], + "xrefs" : [ { + "val" : "AAO:0010411" }, { - "val" : "VHOG:0000723" + "val" : "EFO:0003526" }, { - "val" : "WBbt:0005736" + "val" : "EMAPA:32685" }, { - "val" : "Wikipedia:Excretory_system" + "val" : "NCIT:C34161" }, { - "val" : "XAO:0000143" + "val" : "TAO:0000360" }, { - "val" : "ZFA:0000163" + "val" : "XAO:0000337" }, { - "val" : "galen:UrinaryTract" + "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_110815" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "lbl" : "circulatory system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "lbl" : "cardiac chamber", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].", - "xrefs" : [ "Wikipedia:Circulatory_system" ] + "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", + "xrefs" : [ "GO:0003205" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "systema cardiovasculare", - "xrefs" : [ "Wikipedia:Circulatory_system" ] + "pred" : "hasExactSynonym", + "val" : "chamber of heart" + }, { + "pred" : "hasExactSynonym", + "val" : "heart chamber" } ], "xrefs" : [ { - "val" : "AAO:0000959" - }, { - "val" : "CALOHA:TS-2103" - }, { - "val" : "VHOG:0001248" + "val" : "FMA:7095" }, { - "val" : "Wikipedia:Circulatory_system" + "val" : "SCTID:276456008" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6073" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001015", - "lbl" : "musculature", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004176", + "lbl" : "external genitalia", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A subdivision of the muscular system corresponding to a subdisivision of an organism.", - "xrefs" : [ "Wikipedia:Muscular_system", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "The external genitalia are the outer sex organs, such as the penis or vulva in mammals.", + "xrefs" : [ "GO:0035261" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "muscle group" - }, { - "pred" : "hasExactSynonym", - "val" : "muscles set" - }, { - "pred" : "hasExactSynonym", - "val" : "musculature" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "musculi", - "xrefs" : [ "FMA:32558", "FMA:TA" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of muscles", - "xrefs" : [ "FMA:32558" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of skeletal muscles", - "xrefs" : [ "MA:0000165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle system" + "val" : "external genitalia" }, { "pred" : "hasRelatedSynonym", - "val" : "muscles" + "val" : "external reproductive organ" }, { "pred" : "hasRelatedSynonym", - "val" : "musculature system" + "val" : "external sex organ" } ], "xrefs" : [ { - "val" : "BTO:0000887" - }, { - "val" : "EFO:0001949" - }, { - "val" : "EMAPA:35577" - }, { - "val" : "FMA:32558" - }, { - "val" : "MA:0000165" - }, { - "val" : "NCIT:C13056" - }, { - "val" : "TAO:0000548" - }, { - "val" : "UMLS:C0026845" - }, { - "val" : "VSAO:0005038" - }, { - "val" : "WBbt:0005737" - }, { - "val" : "Wikipedia:Muscular_system" + "val" : "FMA:45643" }, { - "val" : "ZFA:0000548" + "val" : "SCTID:362207005" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "lbl" : "nervous system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004188", + "lbl" : "glomerular epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", - "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] + "val" : "The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.", + "xrefs" : [ "GO:0072010" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "neurological system", - "xrefs" : [ "GO:0050877" ] + "val" : "epithelium of glomerulus" }, { - "pred" : "hasNarrowSynonym", - "val" : "nerve net", - "xrefs" : [ "Wikipedia:Nerve_net" ] + "pred" : "hasExactSynonym", + "val" : "epithelium of kidney glomerulus" + }, { + "pred" : "hasExactSynonym", + "val" : "epithelium of renal glomerulus" + }, { + "pred" : "hasExactSynonym", + "val" : "kidney glomerular epithelium", + "xrefs" : [ "MA:0002847" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "systema nervosum", - "xrefs" : [ "Wikipedia:Nervous_system" ] + "val" : "glomerular epithelial cell", + "xrefs" : [ "BTO:0001515" ] } ], "xrefs" : [ { - "val" : "AAO:0000324" - }, { - "val" : "BILA:0000079" - }, { - "val" : "BIRNLEX:844" - }, { - "val" : "BTO:0001484" - }, { - "val" : "CALOHA:TS-1313" - }, { - "val" : "EFO:0000802" - }, { - "val" : "EHDAA2:0001246" - }, { - "val" : "EHDAA:826" - }, { - "val" : "EMAPA:16469" - }, { - "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" - }, { - "val" : "FMA:7157" - }, { - "val" : "GAID:466" - }, { - "val" : "MA:0000016" - }, { - "val" : "MAT:0000026" - }, { - "val" : "MESH:D009420" - }, { - "val" : "MIAA:0000026" - }, { - "val" : "NCIT:C12755" - }, { - "val" : "SCTID:278196006" - }, { - "val" : "TAO:0000396" - }, { - "val" : "UMLS:C0027763" - }, { - "val" : "VHOG:0000402" - }, { - "val" : "WBbt:0005735" - }, { - "val" : "Wikipedia:Nervous_system" - }, { - "val" : "XAO:0000177" + "val" : "BTO:0001515" }, { - "val" : "ZFA:0000396" + "val" : "EMAPA:35458" }, { - "val" : "neuronames:3236" + "val" : "MA:0002847" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check - GO says outer, BTO says inner. Make this a superclass" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "lbl" : "central nervous system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004190", + "lbl" : "renal glomerulus vasculature", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.", - "xrefs" : [ "GO:0021551", "http://www.frontiersinzoology.com/content/7/1/29", "https://sourceforge.net/p/geneontology/ontology-requests/11422/" ] + "val" : "The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.", + "xrefs" : [ "GO:0072012" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasExactSynonym", - "val" : "CNS" + "val" : "glomerulus vasculature", + "xrefs" : [ "OBOL:automatic" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "systema nervosum centrale", - "xrefs" : [ "FMA:55675", "FMA:TA" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "cerebrospinal axis", - "xrefs" : [ "FMA:55675" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "neuraxis", - "xrefs" : [ "FMA:55675" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000090" - }, { - "val" : "BAMS:CNS" - }, { - "val" : "BILA:0000080" - }, { - "val" : "BIRNLEX:1099" - }, { - "val" : "BTO:0000227" - }, { - "val" : "CALOHA:TS-0150" - }, { - "val" : "EFO:0000908" - }, { - "val" : "EHDAA2:0000225" - }, { - "val" : "EHDAA:828" - }, { - "val" : "EMAPA:16470" - }, { - "val" : "EMAPA:16754" - }, { - "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" - }, { - "val" : "FMA:55675" - }, { - "val" : "GAID:570" - }, { - "val" : "MA:0000167" - }, { - "val" : "MAT:0000457" - }, { - "val" : "MESH:D002490" - }, { - "val" : "NCIT:C12438" - }, { - "val" : "SCTID:278199004" - }, { - "val" : "TAO:0000012" - }, { - "val" : "UMLS:C0927232" - }, { - "val" : "VHOG:0000293" - }, { - "val" : "Wikipedia:Central_nervous_system" + "val" : "renal glomerulus vascular network", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "XAO:0000215" + "pred" : "hasExactSynonym", + "val" : "renal glomerulus vasculature", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "ZFA:0000012" + "pred" : "hasExactSynonym", + "val" : "vascular network of renal glomerulus", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "neuronames:854" + "pred" : "hasExactSynonym", + "val" : "vasculature of renal glomerulus", + "xrefs" : [ "OBOL:automatic" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -21640,241 +23094,235 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001041", - "lbl" : "foregut", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004198", + "lbl" : "comma-shaped body", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anterior subdivision of a digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron.", + "xrefs" : [ "GO:0072049" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "praeenteron", - "xrefs" : [ "Wikipedia:Foregut" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "proenteron", - "xrefs" : [ "Wikipedia:Foregut" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasExactSynonym", + "val" : "CSB" } ], "xrefs" : [ { - "val" : "AAO:0011042" - }, { - "val" : "BILA:0000085" - }, { - "val" : "BTO:0000507" - }, { - "val" : "EHDAA2:0000557" - }, { - "val" : "EHDAA:520" - }, { - "val" : "EMAPA:16548" - }, { - "val" : "FBbt:00005379" - }, { - "val" : "FMA:45616" - }, { - "val" : "MA:0001526" - }, { - "val" : "NCIT:C34180" - }, { - "val" : "SCTID:361409009" - }, { - "val" : "TGMA:0001014" - }, { - "val" : "UMLS:C0231051" - }, { - "val" : "VHOG:0000285" - }, { - "val" : "Wikipedia:Foregut" + "val" : "EMAPA:27681" }, { - "val" : "XAO:0000232" + "val" : "ZFA:0005588" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001045", - "lbl" : "midgut", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004199", + "lbl" : "S-shaped body", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].", - "xrefs" : [ "GO:0007494", "Wikipedia:Midgut" ] + "val" : "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.", + "xrefs" : [ "GO:0072050" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "mesenteron", - "xrefs" : [ "Wikipedia:Midgut" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasExactSynonym", + "val" : "SSB" + }, { + "pred" : "hasExactSynonym", + "val" : "stage II nephron", + "xrefs" : [ "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] } ], "xrefs" : [ { - "val" : "BILA:0000086" - }, { - "val" : "BTO:0000863" - }, { - "val" : "EFO:0001950" - }, { - "val" : "EHDAA2:0001185" - }, { - "val" : "EHDAA:983" - }, { - "val" : "EMAPA:16255" - }, { - "val" : "FBbt:00005383" - }, { - "val" : "FMA:45617" - }, { - "val" : "MA:0001564" - }, { - "val" : "NCIT:C34210" - }, { - "val" : "SCTID:361410004" - }, { - "val" : "TGMA:0001036" - }, { - "val" : "UMLS:C0231052" - }, { - "val" : "VHOG:0000290" - }, { - "val" : "Wikipedia:Midgut" + "val" : "EMAPA:27756" }, { - "val" : "XAO:0000103" + "val" : "ZFA:0005589" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" + "val" : "TODO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001046", - "lbl" : "hindgut", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004200", + "lbl" : "kidney pyramid", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The caudalmost subdivision of a digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.", + "xrefs" : [ "GO:0072056", "http://anatomy.uams.edu/anatomyhtml/kidney.html" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "pyramid", + "xrefs" : [ "GO:0072056" ] + }, { + "pred" : "hasExactSynonym", + "val" : "Malpighian pyramid", + "xrefs" : [ "Wikipedia:Renal_pyramids" ] + }, { + "pred" : "hasExactSynonym", + "val" : "renal pyramid", + "xrefs" : [ "Wikipedia:Renal_pyramids" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", + "pred" : "hasRelatedSynonym", + "val" : "Malphigian pyramid", + "xrefs" : [ "BTO:0003926" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "Malpighian pyramid" + }, { + "pred" : "hasRelatedSynonym", + "val" : "medullary pyramid" + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", + "pred" : "hasRelatedSynonym", + "val" : "pyramid of Malphigi", + "xrefs" : [ "ncithesaurus:Pyramid_of_Malpighi" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "pyramid of Malpighi", + "xrefs" : [ "UBERON:cjm" ] + }, { "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "metenteron", - "xrefs" : [ "Wikipedia:Hindgut" ] + "val" : "pyramides renales", + "xrefs" : [ "Wikipedia:Renal_pyramids" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "pyramis renalis", + "xrefs" : [ "BTO:0003926" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "renal medullary region", + "xrefs" : [ "FMA:258870" ] } ], "xrefs" : [ { - "val" : "AAO:0011052" - }, { - "val" : "BILA:0000087" + "val" : "BTO:0003926" }, { - "val" : "BTO:0000510" + "val" : "FMA:258870" }, { - "val" : "EHDAA2:0000779" + "val" : "MA:0001654" }, { - "val" : "EHDAA:975" + "val" : "NCIT:C12886" }, { - "val" : "EMAPA:16715" + "val" : "NCIT:C33436" }, { - "val" : "FBbt:00005384" + "val" : "SCTID:361328001" }, { - "val" : "FMA:45618" + "val" : "UMLS:C0227629" }, { - "val" : "MA:0001527" + "val" : "UMLS:C1514613" }, { - "val" : "NCIT:C34188" + "val" : "Wikipedia:Renal_pyramids" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "SCTID:362856002" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0002449" }, { - "val" : "TGMA:0001020" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0005098" }, { - "val" : "UMLS:C0231053" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "val" : "VHOG:0000459" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" }, { - "val" : "Wikipedia:Hindgut" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" }, { - "val" : "XAO:0000104" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" + "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001048", - "lbl" : "primordium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004202", + "lbl" : "kidney outer medulla outer stripe", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. 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It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesenchyme of nephron", + "xrefs" : [ "OBOL:automatic" ] }, { - "val" : "XAO:0003043" + "pred" : "hasExactSynonym", + "val" : "nephron mesenchyme", + "xrefs" : [ "OBOL:automatic" ] } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -21882,204 +23330,169 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001049", - "lbl" : "neural tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0004209", + "lbl" : "renal vesicle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].", - "xrefs" : [ "Wikipedia:Neural_tube" ] + "val" : "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.", + "xrefs" : [ "GO:0072077" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural primordium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive central nervous system" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tubus neuralis", - "xrefs" : [ "Wikipedia:Neural_tube" ] + "pred" : "hasExactSynonym", + "val" : "stage I nephron", + "xrefs" : [ "ZFA:0005586", "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] } ], - "xrefs" : [ { - "val" : "AAO:0010617" - }, { - "val" : "BTO:0001057" - }, { - "val" : "CALOHA:TS-2371" - }, { - "val" : "DHBA:10154" - }, { - "val" : "EHDAA2:0001254" - }, { - "val" : "EHDAA:2869" - }, { - "val" : "EHDAA:908" - }, { - "val" : "EMAPA:16164" - }, { - "val" : "EMAPA:16757" - }, { - "val" : "FMA:293882" - }, { - "val" : "MAT:0000069" - }, { - "val" : "MIAA:0000069" - }, { - "val" : "NCIT:C34226" - }, { - "val" : "SCTID:362852000" - }, { - "val" : "TAO:0001135" - }, { - "val" : "UMLS:C0231024" - }, { - "val" : "VHOG:0000307" - }, { - "val" : "Wikipedia:Neural_tube" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. 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Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001637", - "lbl" : "artery", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005167", + "lbl" : "papillary duct", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].", - "xrefs" : [ "AEO:JB" ] + "val" : "The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx.", + "xrefs" : [ "http://encyclopedia.thefreedictionary.com/" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "arterial subtree" + "val" : "papillary duct" }, { "pred" : "hasExactSynonym", - "val" : "arterial tree organ part" + "val" : "papillary duct of kidney" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "arteries", - "xrefs" : [ "TAO:0000005" ] + "val" : "renal papillary duct" }, { "pred" : "hasRelatedSynonym", - "val" : "arterial system" + "val" : "Bellini's duct", + "xrefs" : [ "MP:0011331" ] }, { "pred" : "hasRelatedSynonym", - "val" : "arterial vessel" + "val" : "duct of Bellini" } ], "xrefs" : [ { - "val" : "AAO:0010211" - }, { - "val" : "AEO:0000208" - }, { - "val" : "BTO:0000573" - }, { - "val" : "CALOHA:TS-0054" - }, { - "val" : "EFO:0000814" - }, { - "val" : "EHDAA2:0003253" - }, { - "val" : "EMAPA:35147" - }, { - "val" : "EV:0100026" - }, { - "val" : "FMA:50720" - }, { - "val" : "GAID:468" - }, { - "val" : "MA:0000064" - }, { - "val" : "MAT:0000034" - }, { - "val" : "MESH:D001158" - }, { - "val" : "MIAA:0000034" - }, { - "val" : "NCIT:C12372" - }, { - "val" : "SCTID:362877004" - }, { - "val" : "TAO:0000005" - }, { - "val" : "UMLS:C0003842" - }, { - "val" : "VHOG:0001251" + "val" : "BTO:0004540" }, { - "val" : "Wikipedia:Artery" + "val" : "EMAPA:35655" }, { - "val" : "XAO:0000114" + "val" : "MA:0001646" }, { - "val" : "ZFA:0000005" + "val" : "SCTID:110623009" }, { - "val" : "galen:Artery" + "val" : "Wikipedia:Duct_of_Bellini" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001638", - "lbl" : "vein", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005169", + "lbl" : "interstitial tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the tubular branching vessels that carry blood from the capillaries toward the heart.", - "xrefs" : [ "Wikipedia:Vein" ] + "val" : "Connective tissue between the cellular elements of a structure.", + "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/tissue" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "venous subtree" - }, { - "pred" : "hasBroadSynonym", - "val" : "venous vessel" - }, { "pred" : "hasExactSynonym", - "val" : "venous tree organ part" - }, { - "pred" : "hasRelatedSynonym", - "val" : "vascular element", - "xrefs" : [ "EMAPA:th" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "vena", - "xrefs" : [ "Wikipedia:Vein" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "venae", - "xrefs" : [ "VHOG:0001743" ] + "val" : "interstitium" } ], "xrefs" : [ { - "val" : "AAO:0010212" - }, { - "val" : "AEO:0000209" - }, { - "val" : "BTO:0000234" - }, { - "val" : "CALOHA:TS-1108" - }, { - "val" : "EFO:0000816" - }, { - "val" : "EHDAA2:0003254" - }, { - "val" : "EMAPA:35906" - }, { - "val" : "EV:0100031" - }, { - "val" : "FMA:50723" - }, { - "val" : "GAID:492" - }, { - "val" : "MA:0000067" - }, { - "val" : "MAT:0000037" - }, { - "val" : "MESH:D014680" - }, { - "val" : "MIAA:0000037" - }, { - "val" : "NCIT:C12814" - }, { - "val" : "SCTID:181367001" - }, { - "val" : "TAO:0000082" - }, { - "val" : "UMLS:C0042449" - }, { - "val" : "VHOG:0001743" - }, { - "val" : "Wikipedia:Vein" - }, { - "val" : "XAO:0000115" - }, { - "val" : "ZFA:0000082" + "val" : "FMA:86301" }, { - "val" : "galen:Vein" + "val" : "SCTID:85293002" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check with MA - vein vs venous blood vessel" + "val" : "specify differentia from stroma" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001851", - "lbl" : "cortex", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005172", + "lbl" : "abdomen element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Outermost layer of an organ[WP].", - "xrefs" : [ "Wikipedia:Cortex_(anatomy)" ] + "val" : "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "cortex", - "xrefs" : [ "FMA:61109" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cortex of organ" + "val" : "abdomen organ", + "xrefs" : [ "MA:0000522" ] } ], "xrefs" : [ { - "val" : "EFO:0000383" - }, { - "val" : "EHDAA:9344" - }, { - "val" : "FMA:61109" - }, { - "val" : "Wikipedia:Cortex_(anatomy)" + "val" : "MA:0000522" }, { - "val" : "galen:Cortex" + "val" : "SCTID:272631008" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -23807,56 +25011,24 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001969", - "lbl" : "blood plasma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005173", + "lbl" : "abdominal segment element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The liquid component of blood, in which erythrocytes are suspended.", + "val" : "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.", "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "plasma", - "xrefs" : [ "MA:0002501" ] - }, { - "pred" : "hasBroadSynonym", - "val" : "portion of plasma", - "xrefs" : [ "FMA:62970" ] - }, { "pred" : "hasExactSynonym", - "val" : "blood plasm" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of blood plasma" + "val" : "abdominal segment organ", + "xrefs" : [ "MA:0000529" ] } ], "xrefs" : [ { - "val" : "BTO:0000131" - }, { - "val" : "CALOHA:TS-0800" - }, { - "val" : "EFO:0001905" - }, { - "val" : "EMAPA:35690" - }, { - "val" : "FMA:62970" - }, { - "val" : "GAID:1178" - }, { - "val" : "MA:0002501" - }, { - "val" : "MAT:0000052" - }, { - "val" : "MESH:D010949" - }, { - "val" : "MIAA:0000052" - }, { - "val" : "NCIT:C13356" - }, { - "val" : "UMLS:C0032105" + "val" : "EMAPA:37062" }, { - "val" : "Wikipedia:Blood_plasma" + "val" : "MA:0000529" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -23864,411 +25036,340 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001979", - "lbl" : "venule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", + "lbl" : "trunk region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins.", - "xrefs" : [ "MESH:A07.231.432.952", "MP:0004125" ] + "val" : "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "venula", - "xrefs" : [ "Wikipedia:Venule" ] + "pred" : "hasExactSynonym", + "val" : "trunk organ", + "xrefs" : [ "MA:0000516" ] } ], "xrefs" : [ { - "val" : "BTO:0002626" - }, { - "val" : "EMAPA:35917" - }, { - "val" : "FMA:63130" - }, { - "val" : "MA:0000071" - }, { - "val" : "MESH:D014699" - }, { - "val" : "NCIT:C12818" - }, { - "val" : "SCTID:341687009" - }, { - "val" : "TAO:0005315" - }, { - "val" : "UMLS:C0042520" - }, { - "val" : "VHOG:0001765" - }, { - "val" : "Wikipedia:Venule" + "val" : "EMAPA:37270" }, { - "val" : "ZFA:0005315" + "val" : "MA:0000516" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001980", - "lbl" : "arteriole", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005178", + "lbl" : "thoracic cavity element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The smallest division of the artery located between the muscular arteries and the capillaries[GO].", - "xrefs" : [ "GO:0014830" ] + "val" : "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "arteriola", - "xrefs" : [ "Wikipedia:Arteriole" ] + "pred" : "hasExactSynonym", + "val" : "thoracic cavity organ", + "xrefs" : [ "MA:0000557" ] } ], "xrefs" : [ { - "val" : "AAO:0010253" - }, { - "val" : "BTO:0001997" - }, { - "val" : "EMAPA:35146" - }, { - "val" : "FMA:63182" - }, { - "val" : "MA:0000063" - }, { - "val" : "MESH:D001160" - }, { - "val" : "NCIT:C12672" - }, { - "val" : "SCTID:337724002" - }, { - "val" : "TAO:0002138" - }, { - "val" : "UMLS:C0003847" - }, { - "val" : "VHOG:0001763" - }, { - "val" : "Wikipedia:Arteriole" + "val" : "EMAPA:37273" }, { - "val" : "ZFA:0005255" + "val" : "MA:0000557" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001981", - "lbl" : "blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005179", + "lbl" : "pelvic region element", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A vessel through which blood circulates in the body.", - "xrefs" : [ "BTO:0001102", "Wikipedia:Blood_vessel" ] + "val" : "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "vascular element", - "xrefs" : [ "EMAPA:35993" ] + "pred" : "hasExactSynonym", + "val" : "pelvic element" }, { "pred" : "hasExactSynonym", - "val" : "region of vascular tree organ", - "xrefs" : [ "FMA:50722" ] + "val" : "pelvis organ", + "xrefs" : [ "MA:0000543" ] }, { "pred" : "hasExactSynonym", - "val" : "vascular tree organ region", - "xrefs" : [ "FMA:50722" ] + "val" : "pelvis region organ" + } ], + "xrefs" : [ { + "val" : "EMAPA:37275" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "val" : "MA:0000543" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", + "lbl" : "thoracic segment organ", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "synonyms" : [ { "pred" : "hasRelatedSynonym", - "val" : "vas sanguineum", - "xrefs" : [ "Wikipedia:Blood_vessel" ] + "val" : "upper body organ", + "xrefs" : [ "MA:0000563" ] } ], "xrefs" : [ { - "val" : "AAO:0011004" - }, { - "val" : "AEO:0000207" - }, { - "val" : "BTO:0001102" - }, { - "val" : "CALOHA:TS-0080" - }, { - "val" : "EFO:0000817" - }, { - "val" : "EHDAA2:0003252" - }, { - "val" : "EHDAA:240" - }, { - "val" : "EMAPA:32743" - }, { - "val" : "EMAPA:35993" - }, { - "val" : "FMA:50722" - }, { - "val" : "FMA:63183" - }, { - "val" : "GAID:169" - }, { - "val" : "MA:0000060" - }, { - "val" : "MAT:0000393" - }, { - "val" : "MESH:D001808" - }, { - "val" : "NCIT:C12679" - }, { - "val" : "NLXANAT:090901" - }, { - "val" : "SCTID:361097006" - }, { - "val" : "TAO:0002137" - }, { - "val" : "UMLS:C0005847" - }, { - "val" : "VHOG:0001250" - }, { - "val" : "Wikipedia:Blood_vessel" - }, { - "val" : "XAO:0001011" + "val" : "EMAPA:37271" }, { - "val" : "ZFA:0005314" + "val" : "MA:0000563" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0001982", - "lbl" : "capillary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005185", + "lbl" : "renal medulla collecting duct", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the smallest blood vessels connecting arterioles with venules.", - "xrefs" : [ "ISBN:0073040584", "Wikipedia:Capillary", "https://github.com/obophenotype/uberon/issues/137" ] + "val" : "The portion of the collecting duct that resides in the renal medulla.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood capillary" + "val" : "kidney medulla collecting duct", + "xrefs" : [ "MA:0002935" ] }, { "pred" : "hasExactSynonym", - "val" : "capillary vessel" + "val" : "medullary collecting duct", + "xrefs" : [ "EMAPA:28061" ] } ], "xrefs" : [ { - "val" : "AAO:0010252" - }, { - "val" : "BTO:0002045" - }, { - "val" : "CALOHA:TS-2006" - }, { - "val" : "EFO:0001906" - }, { - "val" : "EMAPA:35198" + "val" : "BTO:0004536" }, { - "val" : "EV:0100035" + "val" : "EMAPA:28061" }, { - "val" : "FMA:63194" + "val" : "EMAPA:35459" }, { - "val" : "MA:0000065" + "val" : "MA:0002935" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005215", + "lbl" : "kidney interstitium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.", + "xrefs" : [ "DOI:10.1038/ki.1991.49", "PMID:18575881", "http://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "interstitial tissue of kidney" }, { - 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Examples: heart, lung, esophagus, kidney, ovary, spleen.", - "xrefs" : [ "BTO:0001491", "Wikipedia:Viscus", "https://github.com/obophenotype/mouse-anatomy-ontology/issues/14" ] + "val" : "Portion of tissue that gives rise to the immature gonad.", + "xrefs" : [ "ZFA:0001262" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "visceral organ", - "xrefs" : [ "RETIRED_EHDAA2:0002201" ] + "val" : "future gonad", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "visceral organ system", - "xrefs" : [ "MA:0000019" ] + "val" : "gonadal primordium", + "xrefs" : [ "ZFA:0001262" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic tissue", - "xrefs" : [ "BTO:0001491" ] + "pred" : "hasExactSynonym", + "val" : "primitive gonad", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "viscera" + "pred" : "hasExactSynonym", + "val" : "undifferentiated gonad", + "xrefs" : [ "ZFA:0001262" ] }, { "pred" : "hasRelatedSynonym", - "val" : "visceral tissue", - "xrefs" : [ "BTO:0001491" ] + "val" : "immature gonad", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { - "val" : "AAO:0010386" - }, { - "val" : "BTO:0001491" - }, { - "val" : "EHDAA:512" - }, { - "val" : "EMAPA:16245" - }, { - "val" : "FMA:7085" - }, { - "val" : "MA:0000019" - }, { - "val" : "MESH:D014781" + "val" : "EFO:0003651" }, { - "val" : "NCIT:C28287" + "val" : "EHDAA:5927" }, { - "val" : "RETIRED_EHDAA2:0002201" + "val" : "EMAPA:17204" }, { - "val" : "SCTID:118760003" + "val" : "RETIRED_EHDAA2:0002148" }, { - "val" : "UMLS:C0042779" + "val" : "TAO:0001262" }, { - "val" : "Wikipedia:Viscus" + "val" : "WBbt:0008366" }, { - "val" : "XAO:0003034" + "val" : "ZFA:0001262" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24338,350 +25428,301 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002078", - "lbl" : "right cardiac atrium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005721", + "lbl" : "pronephric mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve.", - "xrefs" : [ "Wikipedia:Right_atrium", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A mesoderm that has the potential to develop into a pronephros.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "comments" : [ "the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 \"Developmental Biology\", PMID:10720431 \"Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm\"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cardiac right atrium" - }, { - "pred" : "hasExactSynonym", - "val" : "heart right atrium", - "xrefs" : [ "MA:0000075" ] - }, { - "pred" : "hasExactSynonym", - "val" : "right atrium", - "xrefs" : [ "VHOG:0000328" ] + "pred" : "hasRelatedSynonym", + "val" : "pronephric anlage", + "xrefs" : [ "XAO:0000264" ] }, { - "pred" : "hasExactSynonym", - "val" : "right atrium of heart" + "pred" : "hasRelatedSynonym", + "val" : "pronephric bulge", + "xrefs" : [ "XAO:0000264" ] }, { - "pred" : "hasExactSynonym", - "val" : "right cardiac atrium" + "pred" : "hasRelatedSynonym", + "val" : "pronephric mesenchyme", + "xrefs" : [ "XAO:0000264" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "atrium dextrum", - "xrefs" : [ "Wikipedia:Right_atrium" ] + "val" : "pronephric primordium", + "xrefs" : [ "XAO:0000264" ] } ], "xrefs" : [ { - "val" : "AAO:0010248" - }, { - "val" : "BTO:0001703" - }, { - "val" : "EHDAA2:0000290" - }, { - "val" : "EMAPA:17321" - }, { - "val" : "FMA:7096" - }, { - "val" : "MA:0000075" - }, { - "val" : "NCIT:C12868" - }, { - "val" : "SCTID:244383003" + "val" : "AAO:0011090" }, { - "val" : "UMLS:C0225844" + "val" : "EFO:0003479" }, { - "val" : "VHOG:0000328" + "val" : "TAO:0000067" }, { - "val" : "Wikipedia:Right_atrium" + "val" : "VHOG:0001239" }, { - "val" : "XAO:0003192" + "val" : "XAO:0000264" }, { - "val" : "galen:RightAtrium" + "val" : "ZFA:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005749", + "lbl" : "glomerular tuft", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The capillary loops of the kidney that normally function as a filtration unit[MP].", + "xrefs" : [ "MP:0005325", "Wikipedia:Glomerulus", "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "glomerular capillary tuft" }, { - 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"val" : "Cardiac chamber in which blood enters the heart.", - "xrefs" : [ "Wikipedia:Heart_atrium", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.", + "xrefs" : [ "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "atria" - }, { - "pred" : "hasExactSynonym", - "val" : "atrium", - "xrefs" : [ "ZFA:0000471" ] + "val" : "caudal portion of nephrogenic cord", + "xrefs" : [ "OBOL:automatic" ] }, { "pred" : "hasExactSynonym", - "val" : "atrium of heart" + "val" : "caudal region of nephrogenic cord", + "xrefs" : [ "OBOL:automatic" ] }, { - 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"val" : "galen:Atrium" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002090", - "lbl" : "postcranial axial skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "lbl" : "basement membrane of epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].", - "xrefs" : [ "ZFA:0000317", "https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957", "https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834" ] + "val" : "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.", + "xrefs" : [ "Wikipedia:Basement_membrane", "http://orcid.org/0000-0002-6601-2165" ] }, - 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This is being resolved (see tracker items above). Status: MA - fixed." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "axial skeleton", - "xrefs" : [ "FMA:71221", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] + "pred" : "hasExactSynonym", + "val" : "basement membrane of connective tissue", + "xrefs" : [ "FMA:63872" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "post-cranial axial skeleton" + "val" : "membrana basalis", + "xrefs" : [ "Wikipedia:Basement_membrane" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "basement membrane", + "xrefs" : [ "FMA:63872" ] } ], "xrefs" : [ { - "val" : "AAO:0000034" - }, { - "val" : "EFO:0000942" - }, { - "val" : "EHDAA2:0000161" - }, { - "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:37721" - }, { - "val" : "FMA:71221" - }, { - "val" : "MA:0002986" - }, { - "val" : "MAT:0000148" + "val" : "AAO:0010596" }, { - "val" : "MIAA:0000148" + "val" : "FMA:63872" }, { - "val" : "TAO:0000317" + "val" : "GAID:915" }, { - "val" : "VHOG:0000317" + "val" : "NCIT:C13191" }, { - "val" : "VSAO:0000093" + "val" : "SCTID:68989006" }, { - "val" : "XAO:0003073" + "val" : "UMLS:C0004799" }, { - "val" : "ZFA:0000317" + "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002091", - "lbl" : "appendicular skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005777", + "lbl" : "glomerular basement membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].", - "xrefs" : [ "UBERONREF:0000003", "Wikipedia:Appendicular_skeleton", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter.", + "xrefs" : [ "MGI:anna", "MP:0011348" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "appendicular skeleton" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasBroadSynonym", + "val" : "GBM" }, { "pred" : "hasExactSynonym", - "val" : "entire appendicular skeleton", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/59" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasNarrowSynonym", - "val" : "paired fin skeleton" + "val" : "glomerular capillary basement membrane", + "xrefs" : [ "MA:0001659" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "skeleton appendiculare", - "xrefs" : [ "Wikipedia:Appendicular_skeleton" ] + "pred" : "hasExactSynonym", + "val" : "glomerular filtration membrane", + "xrefs" : [ "ZFA:0005285" ] } ], "xrefs" : [ { - "val" : "AAO:0000747" - }, { - "val" : "EFO:0000951" - }, { - "val" : "EMAPA:32729" - }, { - "val" : "FMA:71222" + "val" : "EMAPA:28251" }, { - "val" : "MA:0000290" + "val" : "EMAPA:30965" }, { - "val" : "MAT:0000278" + "val" : "FMA:74274" }, { - "val" : "MIAA:0000278" + "val" : "MA:0001659" }, { - "val" : "NCIT:C49477" + "val" : "NCIT:C32683" }, { - "val" : "SCTID:322050006" + "val" : "SCTID:243897006" }, { - "val" : "UMLS:C0222646" + "val" : "TAO:0005285" }, { - "val" : "VSAO:0000076" + "val" : "UMLS:C0599297" }, { - "val" : "Wikipedia:Appendicular_skeleton" + "val" : "Wikipedia:Glomerular_basement_membrane" }, { - "val" : "XAO:0003166" + "val" : "ZFA:0005285" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002100", - "lbl" : "trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005792", + "lbl" : "nephric ridge", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.", - "xrefs" : [ "TAO:0001115", "UBERONREF:0000006", "Wikipedia:Torso" ] + "val" : "Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.", + "xrefs" : [ "http://cwx.prenhall.com/bookbind/pubbooks/martini10/chapter27/custom2/deluxe-content.html" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracolumbar region" - }, { - "pred" : "hasExactSynonym", - "val" : "torso" - }, { - "pred" : "hasExactSynonym", - "val" : "trunk region", - "xrefs" : [ "XAO:0000054" ] - }, { "pred" : "hasRelatedSynonym", - "val" : "Rumpf", - "xrefs" : [ "BTO:0001493" ] + "val" : "nephric cord", + "xrefs" : [ "VHOG:0001240" ] } ], "xrefs" : [ { - "val" : "AAO:0010339" - }, { - "val" : "BILA:0000116" - }, { - "val" : "BTO:0001493" - }, { - "val" : "CALOHA:TS-1071" - }, { - "val" : "EFO:0000966" - }, { - "val" : "EMAPA:31857" - }, { - "val" : "FMA:7181" - }, { - "val" : "MA:0000004" - }, { - "val" : "MAT:0000296" - }, { - "val" : "MIAA:0000296" - }, { - "val" : "NCIT:C33816" - }, { - "val" : "SCTID:262225004" - }, { - "val" : "TAO:0001115" + "val" : "EHDAA2:0001242" }, { - "val" : "UMLS:C0460005" + "val" : "EHDAA:1015" }, { - "val" : "Wikipedia:Torso" + "val" : "EMAPA:16368" }, { - "val" : "XAO:0000054" + "val" : "VHOG:0001240" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ridge vs cord vs nephrogenic cord vs blastema" }, { - "val" : "XAO:0003025" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0005856", + "lbl" : "developing mesenchymal condensation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A delimited region of dense mesenchyme within looser mesenchyme.", + "xrefs" : [ "AEO:0000148" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesenchyme condensation", + "xrefs" : [ "EMAPA:25351" ] + } ], + "xrefs" : [ { + "val" : "AEO:0000148" }, { - "val" : "ZFA:0001115" + "val" : "EHDAA2_RETIRED:0003148" }, { - "val" : "galen:Trunk" + "val" : "EHDAA:8979" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24689,208 +25730,165 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002113", - "lbl" : "kidney", + "id" : "http://purl.obolibrary.org/obo/UBERON_0005944", + "lbl" : "axial skeleton plus cranial skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.", - "xrefs" : [ "PMID:25140012", "PMID:35003210", "Wikipedia:Kidney", "http://anatomy.uams.edu/anatomyhtml/kidney.html", "https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do" ] + "val" : "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].", + "xrefs" : [ "FMA:71221", "VSAO:0000056", "Wikipedia:Axial_skeleton", "https://github.com/obophenotype/uberon/issues/44", "https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasNarrowSynonym", - "val" : "reniculate kidney", - "xrefs" : [ "Wikipedia:Reniculate_kidney" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "skeleton axiale", + "xrefs" : [ "Wikipedia:Axial_skeleton" ] } ], "xrefs" : [ { - "val" : "AAO:0000250" - }, { - "val" : "BTO:0000671" - }, { - "val" : "CALOHA:TS-0510" + "val" : "AAO:0000963" }, { - "val" : "GAID:423" + "val" : "EMAPA:17214" }, { - "val" : "MAT:0000119" + "val" : "MA:0000308" }, { - "val" : "MESH:D007668" + "val" : "NCIT:C32172" }, { - "val" : "MIAA:0000119" + "val" : "SCTID:361725000" }, { - "val" : "UMLS:C0022646" + "val" : "UMLS:C0222645" }, { - "val" : "Wikipedia:Kidney" + "val" : "VSAO:0000056" }, { - "val" : "XAO:0003267" + "val" : "Wikipedia:Axial_skeleton" }, { - "val" : "galen:Kidney" + "val" : "XAO:0004011" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-7655-4833" - }, { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-2804-127X" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002120", - "lbl" : "pronephros", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006217", + "lbl" : "cloacal membrane", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].", - "xrefs" : [ "GO:0048793", "Wikipedia:Pronephros" ] + "val" : "The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.", + "xrefs" : [ "MP:0011837", "MP:anna", "Wikipedia:Cloacal_membrane" ] }, - "comments" : [ "Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "pronephric kidney", - "xrefs" : [ "XAO:0002000" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "archinephron", - "xrefs" : [ "BTO:0001541" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic kidney", - "xrefs" : [ "BTO:0001541" ] + "val" : "embryonic cloacal membrane" }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasRelatedSynonym", - "val" : "pronephron", - "xrefs" : [ "BTO:0001541" ] + "val" : "membrana cloacalis", + "xrefs" : [ "Wikipedia:Cloacal_membrane" ] } ], "xrefs" : [ { - "val" : "AAO:0011089" - }, { - "val" : "BTO:0001541" - }, { - "val" : "EFO:0000927" - }, { - "val" : "EHDAA2:0001570" - }, { - "val" : "EHDAA:1017" - }, { - "val" : "EMAPA:16579" - }, { - "val" : "FMA:72170" - }, { - "val" : "MAT:0000117" + "val" : "EHDAA2:0000257" }, { - "val" : "MIAA:0000117" + "val" : "EHDAA:214" }, { - "val" : "NCIT:C34280" + "val" : "EHDAA:2933" }, { - "val" : "SCTID:308804007" + "val" : "EMAPA:16832" }, { - "val" : "TAO:0000151" + "val" : "FMA:295525" }, { - "val" : "UMLS:C0231048" + "val" : "NCIT:C34128" }, { - "val" : "VHOG:0000037" + "val" : "SCTID:308826008" }, { - "val" : "Wikipedia:Pronephros" + "val" : "UMLS:C0231056" }, { - "val" : "XAO:0002000" + "val" : "VHOG:0001198" }, { - "val" : "ZFA:0000151" + "val" : "Wikipedia:Cloacal_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005794" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "lbl" : "hemolymphoid system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006267", + "lbl" : "notochordal plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.", + "xrefs" : [ "VHOG:0001212" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "hematolymphoid system" - }, { - "pred" : "hasExactSynonym", - "val" : "lymphomyeloid complex" - }, { - "pred" : "hasRelatedSynonym", - "val" : "haemolymphoid system" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "xrefs" : [ { - "val" : "CALOHA:TS-2018" + "val" : "EHDAA2:0001278" }, { - "val" : "EHDAA2:0004615" + "val" : "EHDAA:264" }, { - "val" : "EMAPA:18765" + "val" : "EMAPA:16101" }, { - "val" : "FMA:74562" + "val" : "NCIT:C34231" }, { - "val" : "MA:0000013" + "val" : "UMLS:C1518429" + }, { + "val" : "VHOG:0001212" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "TODO - check ordering; awaiting confirmation from JB" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002201", - "lbl" : "vasculature of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006268", + "lbl" : "notochordal process", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A vasculature that is part of a trunk [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.", + "xrefs" : [ "http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "comments" : [ "The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "torso vascular network", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "torso vasculature", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "chordamesoderm" }, { - "pred" : "hasExactSynonym", - "val" : "trunk vascular network", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "presumptive notochord" + } ], + "xrefs" : [ { + "val" : "EHDAA2:0001279" }, { - "pred" : "hasExactSynonym", - "val" : "trunk vasculature" + "val" : "EHDAA:224" }, { - "pred" : "hasExactSynonym", - "val" : "vascular network of torso", - "xrefs" : [ "OBOL:automatic" ] + "val" : "EMAPA:16102" }, { - "pred" : "hasExactSynonym", - "val" : "vascular network of trunk", - "xrefs" : [ "OBOL:automatic" ] + "val" : "FMA:293135" }, { - "pred" : "hasExactSynonym", - "val" : "vasculature of torso", - "xrefs" : [ "OBOL:automatic" ] - } ], - "xrefs" : [ { - "val" : "FMA:74712" + "val" : "NCIT:C34232" }, { - "val" : "TAO:0005024" + "val" : "UMLS:C1518430" }, { - "val" : "ZFA:0005024" + "val" : "VHOG:0001213" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24898,49 +25896,37 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002204", - "lbl" : "musculoskeletal system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006314", + "lbl" : "bodily fluid", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that consists of the muscular and skeletal systems.", - "xrefs" : [ "VSAO:0000031", "VSAO:curator", "https://github.com/obophenotype/uberon/issues/77" ] + "val" : "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.", + "xrefs" : [ "MESH:A12.207", "Wikipedia:Body_fluid" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "fluid" + }, { "pred" : "hasExactSynonym", - "val" : "musculo-skeletal system" + "val" : "body fluid", + "xrefs" : [ "GAID:266" ] } ], "xrefs" : [ { - "val" : "AAO:0010546" - }, { - "val" : "CALOHA:TS-1311" - }, { - "val" : "EMAPA:32714" - }, { - "val" : "EV:0100139" - }, { - "val" : "FMA:7482" - }, { - "val" : "GAID:98" - }, { - "val" : "MA:0002418" - }, { - "val" : "MESH:D009141" - }, { - "val" : "NCIT:C12754" + "val" : "BIRNLEX:20" }, { - "val" : "SCTID:278858007" + "val" : "EMAPA:37441" }, { - "val" : "UMLS:C0026860" + "val" : "FMA:280556" }, { - "val" : "VHOG:0001275" + "val" : "GAID:266" }, { - "val" : "VSAO:0000031" + "val" : "MESH:D001826" }, { - "val" : "Wikipedia:Musculoskeletal_system" + "val" : "Wikipedia:Body_fluid" }, { - "val" : "XAO:0000168" + "val" : "galen:BodyFluid" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -24948,109 +25934,76 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002224", - "lbl" : "thoracic cavity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006534", + "lbl" : "renal convoluted tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.", - "xrefs" : [ "UBERON:cjm", "Wikipedia:Thoracic_cavity" ] + "val" : "Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "cavitas thoracis", - "xrefs" : [ "Wikipedia:Thoracic_cavity" ] - }, { - "pred" : "hasExactSynonym", - "val" : "cavity of chest" - }, { - "pred" : "hasExactSynonym", - "val" : "cavity of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "chest cavity" - }, { - "pred" : "hasExactSynonym", - "val" : "pectoral cavity" - }, { "pred" : "hasExactSynonym", - "val" : "space of thoracic compartment", - "xrefs" : [ "FMA:7565" ] + "val" : "convoluted tubule" }, { "pred" : "hasExactSynonym", - "val" : "thoracic lumen" + "val" : "kidney convoluted tubule", + "xrefs" : [ "MA:0001665" ] } ], "xrefs" : [ { - "val" : "EMAPA:36497" - }, { - "val" : "FMA:7565" - }, { - "val" : "GAID:93" - }, { - "val" : "MA:0000032" + "val" : "EMAPA:35725" }, { - "val" : "MESH:D035423" + "val" : "MA:0001665" }, { - "val" : "NCIT:C12905" + "val" : "NCIT:C49479" }, { - "val" : "SCTID:243949006" + "val" : "SCTID:361333002" }, { - "val" : "UMLS:C0230139" + "val" : "UMLS:C1707510" }, { - "val" : "Wikipedia:Thoracic_cavity" + "val" : "Wikipedia:Convoluted_tubule" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002303", - "lbl" : "juxtaglomerular apparatus", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006542", + "lbl" : "outer medulla outer stripe loop of Henle", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP].", - "xrefs" : [ "GO:0072206", "Wikipedia:Juxtaglomerular_apparatus" ] + "val" : "A loop of Henle that is part of a kidney outer medulla outer stripe.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "complexus juxtaglomerularis" + "xrefs" : [ { + "val" : "EMAPA:29665" }, { - "pred" : "hasExactSynonym", - "val" : "juxtaglomerular complex", - "xrefs" : [ "MP:0002829" ] + "val" : "MA:0002630" } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0006544", + "lbl" : "kidney vasculature", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A vasculature that is part of a kidney.", + "xrefs" : [ "OBOL:automatic" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "xrefs" : [ { - "val" : "BTO:0005157" - }, { - "val" : "EMAPA:30449" - }, { - "val" : "FMA:83599" - }, { - "val" : "GAID:432" - }, { - "val" : "MA:0002546" - }, { - "val" : "MESH:D007606" - }, { - "val" : "NCIT:C32891" - }, { - "val" : "SCTID:362219002" + "val" : "EMAPA:28457" }, { - "val" : "UMLS:C0022445" + "val" : "TAO:0005305" }, { - "val" : "Wikipedia:Juxtaglomerular_apparatus" + "val" : "ZFA:0005305" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -25061,489 +26014,225 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002319", - "lbl" : "mesangium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006553", + "lbl" : "renal duct", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries.", - "xrefs" : [ "Wikipedia:Mesangium", "https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/13/" ] + "val" : "A tube in the kidney that collect and transport urine.", + "xrefs" : [ "ZFIN:ZDB-PUB-071029-9" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "xrefs" : [ { - "val" : "BTO:0002494" - }, { - "val" : "EMAPA:36561" - }, { - "val" : "FMA:84139" - }, { - "val" : "MA:0002617" - }, { - "val" : "NCIT:C33101" - }, { - "val" : "UMLS:C0017655" + "val" : "TAO:0005289" }, { - "val" : "Wikipedia:Mesangium" + "val" : "ZFA:0005289" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002321", - "lbl" : "extraglomerular mesangium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006555", + "lbl" : "excretory tube", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus.", - "xrefs" : [ "ISBN:0-683-40008-8", "MP:0011340" ] + "val" : "A tube that is part of a excretory system.", + "xrefs" : [ "OBOL:automatic" ] }, - "comments" : [ "EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus?" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "EMAPA:28278" - }, { - "val" : "FMA:84141" - }, { - "val" : "MA:0002602" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002323", - "lbl" : "coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0006595", + "lbl" : "presumptive endoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. 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The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. 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Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n.", + "xrefs" : [ "CARO:0001002" ] + }, + "comments" : [ "Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism." ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "AAO:0000098" - }, { - "val" : "BTO:0000421" - }, { - "val" : "CALOHA:TS-2009" - }, { - "val" : "EFO:0000952" - }, { - "val" : "EMAPA:35251" - }, { - "val" : "FMA:9640" - }, { - "val" : "GAID:100" - }, { - "val" : "MA:0000011" - }, { - "val" : "MAT:0000301" - }, { - "val" : "MESH:D003238" - }, { - "val" : "MIAA:0000301" - }, { - "val" : "NCIT:C12374" - }, { - "val" : "SCTID:361919005" - }, { - "val" : "TAO:0001641" + "val" : "BILA:0000010" }, { - "val" : "UMLS:C0009780" + "val" : "CARO:0001002" }, { - "val" : "VSAO:0000017" + "val" : "EHDAA2_RETIRED:0003192" }, { - "val" : "XAO:0001017" + "val" : "FMA:24137" }, { - "val" : "ZFA:0001632" + "val" : "NCIT:C34022" }, { - "val" : "galen:ConnectiveTissue" + "val" : "UMLS:C1515977" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "lbl" : "muscle tissue", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "lbl" : "cardiogenic splanchnic mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].", - "xrefs" : [ "GO:0060537", "Wikipedia:Muscle_tissue", "https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764" ] + "val" : "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].", + "xrefs" : [ "XAO:0000235", "http://www.drugs.com/dict/cardiogenic-mesoderm.html", "https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7" ] }, - "comments" : [ "Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasExactSynonym", - "val" : "muscular tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "portion of muscle tissue", - "xrefs" : [ "FMA:9641" ] - }, { "pred" : "hasExactSynonym", - "val" : "textus muscularis" - } ], - "xrefs" : [ { - "val" : "AAO:0000306" + "val" : "cardiogenic splanchnopleure", + "xrefs" : [ "EHDAA2:0000214" ] }, { - "val" : "AEO:0000122" + "pred" : "hasRelatedSynonym", + "val" : "cardiac mesoderm", + "xrefs" : [ "XAO:0000235" ] }, { - "val" : "CALOHA:TS-0642" + "pred" : "hasRelatedSynonym", + "val" : "cardiogenic mesoderm", + "xrefs" : [ "http://www.drugs.com/dict/cardiogenic-mesoderm.html" ] }, { - "val" : "EHDAA2:0003122" + "pred" : "hasRelatedSynonym", + "val" : "cardiogenic region", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "EMAPA:32715" + "pred" : "hasRelatedSynonym", + "val" : "heart primordia", + "xrefs" : [ "XAO:0000235" ] + } ], + "xrefs" : [ { + "val" : "AAO:0011021" }, { - "val" : "FMA:9641" + "val" : "BILA:0000051" }, { - "val" : "MA:0002437" + "val" : "EFO:0000315" }, { - "val" : "MESH:D009132" + "val" : "EHDAA2:0000214" }, { - "val" : "NCIT:C12435" + "val" : "EHDAA:385" }, { - "val" : "SCTID:91727004" + "val" : "FMA:293143" }, { - "val" : "UMLS:C2328219" + "val" : "SCTID:360387000" }, { - "val" : "Wikipedia:Muscle_tissue" + "val" : "VHOG:0001641" }, { - "val" : "galen:MuscleTissue" + "val" : "XAO:0000235" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider FBbt:00005541 ! cardiogenic mesoderm" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "review EHDAA2 placement" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "lbl" : "hematopoietic system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007010", + "lbl" : "cleaving embryo", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that is involved in the production of hematopoietic cells.", - "xrefs" : [ "Wikipedia:Haematopoiesis" ] + "val" : "Organism at the cleavage stage.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "xrefs" : [ { + "val" : "BILA:0000058" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0007026", + "lbl" : "presumptive gut", + "type" : "CLASS", + "meta" : { "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "haematological system" + "val" : "future digestive tract" }, { "pred" : "hasExactSynonym", - "val" : "haemopoietic system" + "val" : "future digestive tube" }, { "pred" : "hasExactSynonym", - "val" : "organa haemopoietica" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Blutbildungssystem", - "xrefs" : [ "BTO:0000570" ] + "val" : "future gut" }, { - "pred" : "hasRelatedSynonym", - "val" : "haematopoietic system" + "pred" : "hasExactSynonym", + "val" : "primitive gut" }, { "pred" : "hasRelatedSynonym", - "val" : "hematological system" + "val" : "embryonic digestive tube" }, { "pred" : "hasRelatedSynonym", - "val" : "hematolymphoid system" + "val" : "primordial digestive tube" }, { "pred" : "hasRelatedSynonym", - "val" : "hemopoietic system" + "val" : "primordial gut" } ], "xrefs" : [ { - "val" : "AAO:0011002" - }, { - "val" : "BTO:0000570" - }, { - "val" : "CALOHA:TS-0449" - }, { - "val" : "EFO:0000798" - }, { - "val" : "EMAPA:35402" - }, { - "val" : "EV:0100045" - }, { - "val" : "FMA:9667" - }, { - "val" : "GAID:1008" - }, { - "val" : "MA:0002434" - }, { - "val" : "MAT:0000022" - }, { - "val" : "MESH:D006413" - }, { - "val" : "MIAA:0000022" - }, { - "val" : "NCIT:C12909" - }, { - "val" : "SCTID:362587009" - }, { - "val" : "TAO:0005023" - }, { - "val" : "UMLS:C0018957" - }, { - "val" : "VHOG:0001624" + "val" : "BILA:0000084" }, { - "val" : "Wikipedia:Haematopoiesis" + "val" : "NCIT:C34268" }, { - "val" : "XAO:0000122" + "val" : "SCTID:360394002" }, { - "val" : "ZFA:0005023" + "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002417", - "lbl" : "abdominal segment of trunk", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007100", + "lbl" : "primary circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The abdominal segment of the torso.", - "xrefs" : [ "Wikipedia:Lumbar" ] + "val" : "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].", + "xrefs" : [ "GO:0007507" ] }, + "comments" : [ "Gene notes: Bmp, Nkx, Gata" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "abdomen/pelvis/perineum", - "xrefs" : [ "MA:0000021" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "lower body", - "xrefs" : [ "MA:0000021" ] + "pred" : "hasNarrowSynonym", + "val" : "dorsal tube", + "xrefs" : [ "Wikipedia:Heart" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "lower trunk", - "xrefs" : [ "FMA:259211" ] + "pred" : "hasNarrowSynonym", + "val" : "heart", + "xrefs" : [ "GO:0007507" ] }, { "pred" : "hasRelatedSynonym", - "val" : "lumbar region", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "adult heart", + "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "EMAPA:35104" - }, { - "val" : "FMA:259211" - }, { - "val" : "MA:0000021" - }, { - "val" : "SCTID:362875007" + "val" : "TADS:0000147" }, { - "val" : "Wikipedia:Lumbar" + "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -25865,86 +26496,54 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002532", - "lbl" : "epiblast (generic)", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007135", + "lbl" : "neural keel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA].", - "xrefs" : [ "Wikipedia:Epiblast", "ZFIN:curator" ] + "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.", + "xrefs" : [ "ZFIN:ZDB-PUB-961014-576" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#early_development", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epiblast", - "xrefs" : [ "VHOG:0000243" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "blastocyst" - }, { "pred" : "hasRelatedSynonym", - "val" : "ectoblast", - "xrefs" : [ "MP:0003886" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "epiblastus", - "xrefs" : [ "Wikipedia:Epiblast" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "primitive ectoderm", - "xrefs" : [ "VHOG:0000243" ] + "val" : "presumptive central nervous system", + "xrefs" : [ "ZFA:0000131" ] } ], "xrefs" : [ { - "val" : "BTO:0004593" - }, { - "val" : "FMA:296704" - }, { - "val" : "MAT:0000067" - }, { - "val" : "MIAA:0000067" + "val" : "EFO:0003497" }, { - "val" : "VHOG:0000243" + "val" : "TAO:0000131" }, { - "val" : "Wikipedia:Epiblast" + "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0002553", - "lbl" : "anatomical cavity", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007282", + "lbl" : "presumptive segmental plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.", - "xrefs" : [ "FMA:67552" ] + "val" : "A presumptive structure that has the potential to develop into a presomitic mesoderm.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "cavity" + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", + "pred" : "hasRelatedSynonym", + "val" : "presumptive segmental plates", + "xrefs" : [ "ZFA:0000053" ] } ], "xrefs" : [ { - "val" : "BIRNLEX:1011" - }, { - "val" : "EMAPA:37442" - }, { - "val" : "FMA:67552" - }, { - "val" : "MA:0002447" + "val" : "EFO:0003421" }, { - "val" : "NCIT:C34007" + "val" : "TAO:0000053" }, { - "val" : "galen:Cavity" + "val" : "ZFA:0000053" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -25952,104 +26551,65 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003059", - "lbl" : "presomitic mesoderm", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007284", + "lbl" : "presumptive neural plate", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.", - "xrefs" : [ "ZFIN:curator" ] + "val" : "A presumptive structure that has the potential to develop into a neural plate.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segmental plate" + "val" : "prospective neuroectoderm", + "xrefs" : [ "ZFA:0000063" ] }, { "pred" : "hasExactSynonym", - "val" : "unsegmented paraxial mesoderm", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "PSM" - }, { - "pred" : "hasRelatedSynonym", - "val" : "presumptive somite mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitogenic mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "somitomeric mesoderm", - "xrefs" : [ "GO:0002075" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "unsegmented mesenchyme", - "xrefs" : [ "VHOG:0000559" ] + "val" : "prospective vegetal ectoderm", + "xrefs" : [ "ZFA:0000063" ] } ], "xrefs" : [ { - "val" : "AAO:0011086" - }, { - "val" : "EFO:0001982" - }, { - "val" : "EMAPA:16189" - }, { - "val" : "EMAPA:16752" - }, { - "val" : "TAO:0000279" - }, { - "val" : "VHOG:0000559" + "val" : "EFO:0003424" }, { - "val" : "XAO:0000057" + "val" : "TAO:0000063" }, { - "val" : "ZFA:0000279" + "val" : "ZFA:0000063" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003060", - "lbl" : "pronephric duct", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007285", + "lbl" : "presumptive paraxial mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].", - "xrefs" : [ "Wikipedia:Pronephric_duct" ] + "val" : "The part of the blastula that has the potential to develop into a paraxial mesoderm.", + "xrefs" : [ "UBERON:cjm", "https://github.com/obophenotype/uberon/issues/1277" ] }, - "comments" : [ "The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "archinephric duct", - "xrefs" : [ "VHOG:0000082" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "ductus pronephricus", - "xrefs" : [ "Wikipedia:Pronephric_duct" ] + "pred" : "hasExactSynonym", + "val" : "future paraxial mesenchyme", + "xrefs" : [ "UBERON:cjm" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "pronephric ducts", - "xrefs" : [ "ZFA:0000150" ] + "pred" : "hasExactSynonym", + "val" : "future paraxial mesoderm" } ], "xrefs" : [ { - "val" : "AAO:0011088" - }, { - "val" : "NCIT:C34279" - }, { - "val" : "SCTID:361406002" - }, { - "val" : "TAO:0000150" - }, { - "val" : "UMLS:C1283945" + "val" : "EFO:0003443" }, { - "val" : "Wikipedia:Pronephric_duct" + "val" : "TAO:0000591" }, { - "val" : "XAO:0000063" + "val" : "XAO:0004134" }, { - "val" : "ZFA:0000150" + "val" : "ZFA:0000591" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26057,60 +26617,26 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "lbl" : "blood island", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007297", + "lbl" : "presumptive pronephric mesoderm", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. 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From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].", - "xrefs" : [ "Wikipedia:Sclerotome", "XB:curator", "https://github.com/obophenotype/uberon/issues/316" ] + "val" : "Anatomical system that consists of all blood and lymph vessels.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasExactSynonym", - "val" : "sclerotomes", - "xrefs" : [ "TAO:0001080" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "sclerotomus", - "xrefs" : [ "Wikipedia:Sclerotome" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "xrefs" : [ { - "val" : "AAO:0010571" - }, { - "val" : "AEO:0000212" - }, { - "val" : "EHDAA2:0003439" - }, { - "val" : "EMAPA:31159" - }, { - "val" : "FMA:295652" - }, { - "val" : "NCIT:C34287" + "val" : "BTO:0001085" }, { - "val" : "TAO:0001080" + "val" : "CALOHA:TS-2053" }, { - "val" : "UMLS:C0183176" + "val" : "EHDAA2:0004520" }, { - "val" : "VHOG:0000680" + "val" : "EMAPA:35905" }, { - "val" : "Wikipedia:Sclerotome" + "val" : "MA:0002718" }, { - "val" : "XAO:0000397" + "val" : "NCIT:C33854" }, { - "val" : "ZFA:0001080" + "val" : "UMLS:C0489903" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider merging with vasculature" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003103", - "lbl" : "compound organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007823", + "lbl" : "appendage girdle region", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.", - "xrefs" : [ "CARO:0000024" ] + "val" : "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).", + "xrefs" : [ "UBERONREF:0000003", "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "organ" - } ], - "xrefs" : [ { - "val" : "AAO:0010015" - }, { - "val" : "AEO:0000024" - }, { - "val" : "BILA:0000024" - }, { - "val" : "CARO:0000024" - }, { - "val" : "EHDAA2:0003024" + "pred" : "hasBroadSynonym", + "val" : "girdle" }, { - "val" : "HAO:0000024" + "pred" : "hasBroadSynonym", + "val" : "girdle region" }, { - "val" : "TADS:0000598" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "fin girdle" }, { - "val" : "TAO:0000496" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "fin girdle region" }, { - "val" : "TGMA:0001837" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "limb girdle" }, { - "val" : "VHOG:0001723" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", + "pred" : "hasRelatedSynonym", + "val" : "limb girdle region" + } ], + "xrefs" : [ { + "val" : "EMAPA:37854" }, { - "val" : "XAO:0003041" + "val" : "FMA:24874" }, { - "val" : "ZFA:0000496" + "val" : "VSAO:0000303" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0007824" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "lbl" : "mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0007832", + "lbl" : "pelvic girdle skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.", - "xrefs" : [ "https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up", "https://en.wikipedia.org/wiki/Mesenchyme", "https://github.com/obophenotype/uberon/issues/1641" ] + "val" : "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.", + "xrefs" : [ "VSAO:0000155", "Wikipedia:Pelvis" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "mesenchymal tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "mesenchyme tissue" + "val" : "pelvic girdle skeleton", + "xrefs" : [ "VSAO:0000155" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of mesenchymal tissue" + "val" : "skeletal parts of pelvic girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "portion of mesenchyme tissue" + "val" : "skeleton of pelvic girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", "pred" : "hasRelatedSynonym", - "val" : "mesenchyma", - "xrefs" : [ "Wikipedia:Mesenchyme" ] + "val" : "pelvic girdle", + "xrefs" : [ "VSAO:0000155" ] } ], "xrefs" : [ { - "val" : "AAO:0010427" + "val" : "AAO:0000426" }, { - "val" : "AEO:0000145" + "val" : "AAO:0000768" }, { - "val" : "BTO:0001393" + "val" : "EFO:0000947" }, { - "val" : "CALOHA:TS-0620" + "val" : "EHDAA2:0001426" }, { - "val" : "EHDAA2:0003145" + "val" : "EHDAA:7149" }, { - "val" : "EV:0100007" + "val" : "EHDAA:8324" }, { - "val" : "NCIT:C13301" + "val" : "EMAPA:18028" }, { - "val" : "TAO:0000393" + "val" : "FMA:87592" }, { - "val" : "UMLS:C0162415" + "val" : "MAT:0000182" }, { - "val" : "VHOG:0000170" + "val" : "MIAA:0000182" }, { - "val" : "Wikipedia:Mesenchyme" + "val" : "TAO:0000565" }, { - "val" : "XAO:0003046" + "val" : "VHOG:0000305" }, { - "val" : "ZFA:0000393" + "val" : "VSAO:0000155" + }, { + "val" : "Wikipedia:Pelvis" + }, { + "val" : "XAO:0003064" + }, { + "val" : "ZFA:0000565" + }, { + "val" : "galen:PelvicGirdle" + }, { + "val" : "http://people.eku.edu/ritchisong/pectoralgirdles.gif" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" + "val" : "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" + "val" : "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003133", - "lbl" : "reproductive organ", + "id" : "http://purl.obolibrary.org/obo/UBERON_0008987", + "lbl" : "renal parenchyma", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organ involved in reproduction.", - "xrefs" : [ "UBERON:xp" ] + "val" : "The functional tissue of the kidney, consisting of the nephrons.", + "xrefs" : [ "BTO:0003604" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "genital organ" - }, { - "pred" : "hasExactSynonym", - "val" : "reproductive system organ" - }, { - "pred" : "hasExactSynonym", - "val" : "sex organ" + "val" : "parenchyma of kidney", + "xrefs" : [ "FMA:15574" ] }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "genitalia" + "val" : "kidney parenchyma", + "xrefs" : [ "BTO:0003604" ] } ], "xrefs" : [ { - "val" : "EMAPA:37731" - }, { - "val" : "MA:0001752" - }, { - "val" : "MESH:D005835" - }, { - "val" : "NCIT:C25177" - }, { - "val" : "SCTID:128181006" - }, { - "val" : "TGMA:0000591" + "val" : "BTO:0003604" }, { - "val" : "UMLS:C0017420" + "val" : "FMA:15574" }, { - "val" : "WBbt:0008422" + "val" : "SCTID:29704000" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26732,49 +27028,30 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003220", - "lbl" : "metanephric mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009035", + "lbl" : "renal straight tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO].", - "xrefs" : [ "GO:0072075", "Wikipedia:Metanephric_blastema" ] + "val" : "Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 \"Developmental Biology\"]" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "metanephric blastema", - "xrefs" : [ "Wikipedia:Metanephric_blastema" ] - }, { - "pred" : "hasExactSynonym", - "val" : "metanephric mesoderm", - "xrefs" : [ "Wikipedia:Metanephric_blastema" ] - }, { - "pred" : "hasExactSynonym", - "val" : "metanephrogenic mesenchyme", - "xrefs" : [ "EHDAA:5021" ] + "val" : "kidney straight tubule", + "xrefs" : [ "MA:0002634" ] }, { "pred" : "hasExactSynonym", - "val" : "metanephros associated mesenchyme", - "xrefs" : [ "RETIRED_EHDAA2:0001139" ] + "val" : "straight tubule" } ], "xrefs" : [ { - "val" : "EHDAA2:0004062" - }, { - "val" : "EHDAA:4041" - }, { - "val" : "EHDAA:5021" - }, { - "val" : "EHDAA:5915" - }, { - "val" : "EMAPA:17375" + "val" : "EMAPA:37489" }, { - "val" : "SCTID:361529008" + "val" : "MA:0002634" }, { - "val" : "VHOG:0000540" + "val" : "SCTID:245151008" }, { - "val" : "Wikipedia:Metanephric_blastema" + "val" : "Wikipedia:Tubuli_seminiferi_recti" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26782,55 +27059,107 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003479", - "lbl" : "thoracic cavity vein", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", + "lbl" : "entire embryonic mesenchyme", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A vein that is part of a thoracic cavity [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Sum total of mesenchyme in the embryo.", + "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "cavity of chest vein", - "xrefs" : [ "OBOL:automatic" ] + "xrefs" : [ { + "val" : "EHDAA2:0001113" }, { - "pred" : "hasExactSynonym", - "val" : "cavity of thorax vein", - "xrefs" : [ "OBOL:automatic" ] + "val" : "EHDAA:177" }, { - "pred" : "hasExactSynonym", - "val" : "chest cavity vein", - "xrefs" : [ "OBOL:automatic" ] + "val" : "EMAPA:16097" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" }, { - "pred" : "hasExactSynonym", - "val" : "pectoral cavity vein", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:0003313" }, { - "pred" : "hasExactSynonym", - "val" : "vein of cavity of chest", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009196", + "lbl" : "indifferent external genitalia", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], + "xrefs" : [ { + "val" : "EHDAA2:0004021" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009201", + "lbl" : "nephric duct", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A nephric duct is a tube that drains a primitive kidney[GO].", + "xrefs" : [ "GO:0072176" ] + }, + "comments" : [ "pronephric duct or mesonephric duct" ], + "xrefs" : [ { + "val" : "EMAPA:16577" }, { + "val" : "Wikipedia:Wolffian_duct" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", + "lbl" : "subdivision of trunk", + "type" : "CLASS", + "meta" : { + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "vein of cavity of thorax", - "xrefs" : [ "OBOL:automatic" ] + "val" : "region of trunk", + "xrefs" : [ "FMA:25054" ] }, { "pred" : "hasExactSynonym", - "val" : "vein of chest cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "trunk subdivision", + "xrefs" : [ "FMA:25054" ] + } ], + "xrefs" : [ { + "val" : "FMA:25054" }, { + "val" : "SCTID:22943007" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", + "lbl" : "trunk paraxial mesoderm", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "vein of pectoral cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "trunk and cervical paraxial mesenchyme", + "xrefs" : [ "EHDAA2:0002094" ] }, { - "pred" : "hasExactSynonym", - "val" : "vein of thoracic cavity", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasRelatedSynonym", + "val" : "trunk paraxial mesenchyme", + "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] } ], "xrefs" : [ { - "val" : "EMAPA:37242" - }, { - "val" : "MA:0001903" + "val" : "EHDAA2:0002094" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26838,21 +27167,43 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003497", - "lbl" : "abdomen blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009773", + "lbl" : "renal tubule", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of an abdomen [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.", + "xrefs" : [ "DOI:10.1371/journal.pone.0099864", "GO:0061333", "GOC:dph", "GOC:mtg_kidney_jan10" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood vessel of abdomen", - "xrefs" : [ "OBOL:automatic" ] + "val" : "renal tubule (generic)", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "tubule of excretory system", + "xrefs" : [ "OBOL:automatic", "https://orcid.org/0000-0002-6601-2165" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0009856", + "lbl" : "sac", + "type" : "CLASS", + "meta" : { + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "pouch" + }, { + "pred" : "hasRelatedSynonym", + "val" : "diverticulum" } ], "xrefs" : [ { - "val" : "MA:0000518" + "val" : "galen:Diverticulum" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26860,20 +27211,22 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003509", - "lbl" : "arterial blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "lbl" : "anterior lateral plate mesoderm", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "comments" : [ "only in MA - supertype of artery, arteriole, aorta." ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "ALPM", + "xrefs" : [ "ZFA:0005041" ] + } ], "xrefs" : [ { - "val" : "EMAPA:35144" + "val" : "EFO:0003704" }, { - "val" : "MA:0000061" + "val" : "TAO:0005041" + }, { + "val" : "ZFA:0005041" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -26881,246 +27234,269 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003513", - "lbl" : "trunk blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009885", + "lbl" : "interlobar artery", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of a trunk [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "An artery that supplies a renal lobe.", + "xrefs" : [ "Wikipedia:Interlobar_arteries", "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "blood vessel of torso", - "xrefs" : [ "OBOL:automatic" ] + "val" : "arteriae interlobares renis", + "xrefs" : [ "FMA:TA" ] }, { "pred" : "hasExactSynonym", - "val" : "blood vessel of trunk", - "xrefs" : [ "OBOL:automatic" ] + "val" : "interlobar artery of kidney", + "xrefs" : [ "FMA:71637" ] }, { "pred" : "hasExactSynonym", - "val" : "torso blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "kidney interlobar artery" + }, { + "pred" : "hasExactSynonym", + "val" : "renal interlobar artery", + "xrefs" : [ "MP:0011355" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "arteriae interlobares renis", + "xrefs" : [ "Wikipedia:Interlobar_arteries" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "interlobar arteries of kidney", + "xrefs" : [ "FMA:71637" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of interlobar arteries of kidney", + "xrefs" : [ "FMA:71637" ] } ], "xrefs" : [ { - "val" : "EMAPA:37237" + "val" : "EMAPA:37091" }, { - "val" : "MA:0000511" + "val" : "FMA:71637" + }, { + "val" : "SCTID:62802007" + }, { + "val" : "Wikipedia:Interlobar_arteries" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003517", - "lbl" : "kidney blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009912", + "lbl" : "anatomical lobe", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of a kidney [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "A portion of an organ, such as the liver, lung, breast, or brain.", + "xrefs" : [ "ncithesaurus:Lobe" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "blood vessel of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "lobus", + "xrefs" : [ "FMA:45728", "FMA:TA" ] } ], "xrefs" : [ { - "val" : "MA:0001682" + "val" : "FMA:45728" }, { - "val" : "TAO:0005306" + "val" : "NCIT:C13393" }, { - "val" : "ZFA:0005306" + "val" : "UMLS:C0796494" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003519", - "lbl" : "thoracic cavity blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0009913", + "lbl" : "renal lobe", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that is part of a thoracic cavity [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP].", + "xrefs" : [ "MP:0011381", "Wikipedia:Renal_lobe" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood vessel of cavity of chest", - "xrefs" : [ "OBOL:automatic" ] + "val" : "kidney lobe", + "xrefs" : [ "MP:0011381" ] }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasExactSynonym", - "val" : "blood vessel of cavity of thorax", - "xrefs" : [ "OBOL:automatic" ] + "val" : "lobi renalis", + "xrefs" : [ "Wikipedia:Renal_lobe" ] }, { "pred" : "hasExactSynonym", - "val" : "blood vessel of chest cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "lobus renalis", + "xrefs" : [ "http://www.mondofacto.com/facts/dictionary?lobus+renalis" ] }, { - "pred" : "hasExactSynonym", - "val" : "blood vessel of pectoral cavity", - "xrefs" : [ "OBOL:automatic" ] + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", + "pred" : "hasRelatedSynonym", + "val" : "lobi renales", + "xrefs" : [ "Wikipedia:Renal_lobe" ] + } ], + "xrefs" : [ { + "val" : "FMA:17881" }, { - "pred" : "hasExactSynonym", - "val" : "blood vessel of thoracic cavity", - "xrefs" : [ "OBOL:automatic" ] + "val" : "NCIT:C32894" }, { - "pred" : "hasExactSynonym", - "val" : "cavity of chest blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "UMLS:C0736382" }, { - "pred" : "hasExactSynonym", - "val" : "cavity of thorax blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Wikipedia:Renal_lobe" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "todo - add has_part relationships." }, { - "pred" : "hasExactSynonym", - "val" : "chest cavity blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { + "pred" : "http://xmlns.com/foaf/0.1/depiction", + "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010000", + "lbl" : "multicellular anatomical structure", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has more than one cell as a part.", + "xrefs" : [ "CARO:0010000" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "pectoral cavity blood vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "multicellular structure", + "xrefs" : [ "FBbt:00100313" ] } ], "xrefs" : [ { - "val" : "EMAPA:37240" + "val" : "CARO:0010000" }, { - "val" : "MA:0000554" + "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003527", - "lbl" : "kidney capillary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010199", + "lbl" : "bona-fide anatomical boundary", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A capillary that is part of a kidney [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "An anatomical boundary that corresponds to some physical discontinuity.", + "xrefs" : [ "CARO:0001004" ] + }, + "comments" : [ "One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "CARO:0001004" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010227", + "lbl" : "future cardiac atrium", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.", + "xrefs" : [ "ZFA:0001718" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood capillary of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary vessel of kidney", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "kidney blood capillary", - "xrefs" : [ "OBOL:automatic" ] + "val" : "presumptive atrium heart tube", + "xrefs" : [ "ZFA:0001718" ] }, { "pred" : "hasExactSynonym", - "val" : "kidney capillary vessel", - "xrefs" : [ "OBOL:automatic" ] + "val" : "primordial atrium", + "xrefs" : [ "FMA:71005" ] }, { "pred" : "hasExactSynonym", - "val" : "renal capillary", - "xrefs" : [ "OBOL:automatic" ] + "val" : "primordial cardiac atrium", + "xrefs" : [ "FMA:71005" ] } ], "xrefs" : [ { - "val" : "EMAPA:31443" + "val" : "FMA:71005" }, { - "val" : "MA:0002586" + "val" : "TAO:0002228" }, { - "val" : "SCTID:275409003" + "val" : "ZFA:0001718" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003644", - "lbl" : "kidney arterial blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "lbl" : "structure with developmental contribution from neural crest", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An arterial blood vessel that is part of a kidney [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "An anatomical structure that has some part that develops from the neural crest.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "kidney arterial system", - "xrefs" : [ "EMAPA:31436" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:31436" - }, { - "val" : "MA:0002578" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003835", - "lbl" : "abdominal segment blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010316", + "lbl" : "germ layer / neural crest", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "abdominal segment of trunk blood vessel", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "blood vessel of abdominal segment of trunk", - "xrefs" : [ "OBOL:automatic" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37057" - }, { - "val" : "MA:0000524" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "lbl" : "future coelemic cavity lumen", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010371", + "lbl" : "ecto-epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An anatomical cavity that has the potential to develop into a coelemic cavity lumen.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Epithelium composed of cells that develops from the ectoderm[FMA,modified].", + "xrefs" : [ "FMA:69064" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "future coelomic cavity lumen" - }, { - "pred" : "hasRelatedSynonym", - "val" : "body cavity precursor" + "val" : "ectoderm-derived epithelium" + } ], + "xrefs" : [ { + "val" : "FMA:69064" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27128,61 +27504,46 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003887", - "lbl" : "intraembryonic coelom", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010377", + "lbl" : "mesenchyme from somatopleure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.", - "xrefs" : [ "MGI:anna", "MP:0012187" ] + "val" : "Mesenchyme that develops_from a somatopleure.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "somatic coelom", - "xrefs" : [ "Wikipedia:Intraembryonic_coelom" ] - } ], "xrefs" : [ { - "val" : "EHDAA:251" - }, { - "val" : "EMAPA:16088" - }, { - "val" : "NCIT:C34195" - }, { - "val" : "UMLS:C1512940" - }, { - "val" : "VHOG:0000316" - }, { - "val" : "Wikipedia:Intraembryonic_coelom" + "val" : "EHDAA2:0001120" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" + "val" : "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "lbl" : "stroma", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010523", + "lbl" : "microcirculatory vessel", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.", + "xrefs" : [ "MESH:A07.231.432", "ZFA:0005251", "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", "pred" : "hasRelatedSynonym", - "val" : "stromal connective tissue" + "val" : "microcirculatory vessels", + "xrefs" : [ "TAO:0005251" ] } ], "xrefs" : [ { - "val" : "FMA:81494" + "val" : "MESH:D055806" }, { - "val" : "NCIT:C67387" + "val" : "TAO:0005251" }, { - "val" : "UMLS:C0927195" + "val" : "ZFA:0005251" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27190,24 +27551,26 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003914", - "lbl" : "epithelial tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010532", + "lbl" : "primitive nephron", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.", - "xrefs" : [ "GO:0060562", "PMID:12526790" ] + "val" : "An epithelial tube that is fated to become a nephron.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial or endothelial tube" - } ], - "xrefs" : [ { - "val" : "AEO:0000114" + "pred" : "hasBroadSynonym", + "val" : "developing nephron" }, { - "val" : "EHDAA2:0003114" + "pred" : "hasBroadSynonym", + "val" : "primitive nephron" }, { - "val" : "FBbt:00007474" + "pred" : "hasExactSynonym", + "val" : "future nephron" + }, { + "pred" : "hasExactSynonym", + "val" : "presumptive nephron" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27215,511 +27578,439 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003918", - "lbl" : "kidney mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010536", + "lbl" : "nephron progenitor", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].", - "xrefs" : [ "GO:0072074" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of kidney" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "check this" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0003920", - "lbl" : "venous blood vessel", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010707", + "lbl" : "appendage girdle complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A blood vessel that carries blood from the capillaries toward the heart.", - "xrefs" : [ "http://www.thefreedictionary.com/venous+blood+vessel" ] + "val" : "An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).", + "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton", "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "Compare to: vein" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "segment of venous tree organ", - "xrefs" : [ "FMA:86188" ] + "val" : "appendage complex", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { "pred" : "hasExactSynonym", - "val" : "venous tree organ segment", - "xrefs" : [ "FMA:86188" ] + "val" : "appendage-girdle complex", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasExactSynonym", + "val" : "appendage/girdle complex", + "xrefs" : [ "VSAO:0000214" ] + }, { + "pred" : "hasExactSynonym", + "val" : "girdle plus limb or fin", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "pred" : "hasRelatedSynonym", + "val" : "limb", + "xrefs" : [ "FMA:7182" ] } ], "xrefs" : [ { - "val" : "EMAPA:35932" + "val" : "EMAPA:37858" }, { - "val" : "FMA:86188" + "val" : "FMA:7182" }, { - "val" : "MA:0000066" + "val" : "VSAO:0000214" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "It is still called a complex when one of the two parts is missing (?) 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There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9114-8737" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2012-04-23T10:46:51Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004087", - "lbl" : "vena cava", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010709", + "lbl" : "pelvic complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.", - "xrefs" : [ "Wikipedia:Venae_cavae", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.", + "xrefs" : [ "VSAO:0000215" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "caval vein" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "venae cavae", - "xrefs" : [ "Wikipedia:Venae_cavae" ] - } ], - "xrefs" : [ { - "val" : "AAO:0010215" - }, { - "val" : "BTO:0001438" - }, { - "val" : "EMAPA:18415" + "pred" : "hasExactSynonym", + "val" : "pelvic appendage/girdle complex", + "xrefs" : [ "VSAO:0000215" ] }, { - "val" : "FMA:321896" + "pred" : "hasExactSynonym", + "val" : "pelvic girdle plus pelvic limb or fin", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "GAID:547" + "pred" : "hasExactSynonym", + "val" : "pelvic girdle plus posterior limb or fin", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "MA:0000068" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "pred" : "hasRelatedSynonym", + "val" : "lower limb", + "xrefs" : [ "FMA:7184" ] }, { - "val" : "MESH:D014684" + "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "pred" : "hasRelatedSynonym", + "val" : "lower limb and pelvic girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, { - "val" : "NCIT:C12817" + "pred" : "hasRelatedSynonym", + "val" : "lower limb and pelvis", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } ], + "xrefs" : [ { + "val" : "EMAPA:37863" }, { - "val" : "SCTID:244405007" + "val" : "FMA:7184" }, { - "val" : "UMLS:C0042460" + "val" : "SCTID:416631005" }, { - "val" : "Wikipedia:Venae_cavae" + "val" : "VSAO:0000215" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004100", - "lbl" : "renal collecting system", + "id" : "http://purl.obolibrary.org/obo/UBERON_0010719", + "lbl" : "girdle skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. 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"val" : "galen:GenitoUrinarySystem" + "val" : "VSAO:0000306" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004134", - "lbl" : "proximal tubule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011585", + "lbl" : "cell condensation", "type" : "CLASS", "meta" : { "definition" : { - "val" : "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO].", - "xrefs" : [ "GO:0072014" ] + "val" : "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).", + "xrefs" : [ "GO_REF:0000034", "PSPUB:0000170", "VSAO:0000006", "http://dx.plos.org/10.1371/journal.pone.0051070" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "kidney proximal tubule", - "xrefs" : [ "MA:0002611" ] - }, { - "pred" : "hasExactSynonym", - "val" : "proximal kidney tubule", - "xrefs" : [ "MESH:A05.810.453.736.560.570" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal proximal tubule" - } ], "xrefs" : [ { - "val" : "BTO:0001498" - }, { - "val" : "CALOHA:TS-0509" - }, { - "val" : "EMAPA:28281" - }, { - "val" : "MA:0002611" + "val" : "VSAO:0000006" }, { - "val" : "MESH:D007687" + "val" : "XAO:0004021" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - ensure definition works across species." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "consider obsoleting, coordinate with VSAO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004135", - "lbl" : "distal tubule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011676", + "lbl" : "subdivision of organism along main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments.", - "xrefs" : [ "GO:0072017" ] + "val" : "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "kidney distal tubule", - "xrefs" : [ "MA:0002633" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal distal tubule" - } ], - "xrefs" : [ { - "val" : "BTO:0000482" - }, { - "val" : "CALOHA:TS-0504" - }, { - "val" : "EMAPA:28387" + "val" : "axial subdivision of organism" }, { - "val" : "MA:0002633" + "pred" : "hasRelatedSynonym", + "val" : "body segment" }, { - "val" : "MESH:D007686" + "pred" : "hasRelatedSynonym", + "val" : "main body segment" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004136", - "lbl" : "intermediate tubule", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", + "lbl" : "embryonic cardiovascular system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules.", - "xrefs" : [ "GO:0072018" ] + "val" : "A cardiovascular system that is part of a conceptus.", + "xrefs" : [ "OBOL:automatic" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "renal intermediate tubule" + "val" : "conceptus cardiovascular system" }, { - "pred" : "hasExactSynonym", - "val" : "tubulus attenuatus", - "xrefs" : [ "FMA:17718" ] + "pred" : "hasRelatedSynonym", + "val" : "embryonic circulatory system" + }, { + "pred" : "hasRelatedSynonym", + "val" : "fetal circulatory system" } ], "xrefs" : [ { - "val" : "FMA:17718" + "val" : "EHDAA2:0000216" + }, { + "val" : "FMA:305965" + }, { + "val" : "NCIT:C34148" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check for applicability across species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004139", - "lbl" : "cardiogenic plate", + "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", + "lbl" : "coelom", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The first recognizable structure derived from the heart field.", - "xrefs" : [ "GO:0003142" ] + "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", + "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "myocardial plate", - "xrefs" : [ "EHDAA2:0000215" ] + "pred" : "hasNarrowSynonym", + "val" : "enterocoelom", + "xrefs" : [ "NCBITaxon:33511" ] }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac crescent", - "xrefs" : [ "EMAPA:16106" ] + "pred" : "hasNarrowSynonym", + "val" : "haemocoelom" + }, { + "pred" : "hasNarrowSynonym", + "val" : "schizocoelom" }, { "pred" : "hasRelatedSynonym", - "val" : "cardiogenic crescent", - "xrefs" : [ "GO:0003142" ] + "val" : "coelem" }, { "pred" : "hasRelatedSynonym", - "val" : "heart rudiment" + "val" : "coelomic cavity", + "xrefs" : [ "EHDAA2:0004731" ] } ], "xrefs" : [ { - "val" : "EHDAA2:0000215" - }, { - "val" : "EMAPA:16106" + "val" : "EHDAA2:0004731" }, { - "val" : "VHOG:0000975" + "val" : "Wikipedia:Coelom" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" + "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004140", - "lbl" : "primary heart field", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012274", + "lbl" : "columnar epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.", - "xrefs" : [ "GO:0003138", "GOC:mtg_heart", "GOC:rl" ] + "val" : "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].", + "xrefs" : [ "Wikipedia:Columnar_epithelium" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "first heart field", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primary heart field", - "xrefs" : [ "PMID:17276708", "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "FHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasRelatedSynonym", - "val" : "PHF", - "xrefs" : [ "XAO:0004185" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "heart field", - "xrefs" : [ "XAO:0004185" ] - } ], "xrefs" : [ { - "val" : "XAO:0004185" + "val" : "Wikipedia:Columnar_epithelium" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27727,42 +28018,23 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004141", - "lbl" : "heart tube", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", + "lbl" : "meso-epithelium", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An epithelial tube that will give rise to the mature heart.", - "xrefs" : [ "GO:0003143", "GOC:mtg_heart" ] + "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "embryonic heart tube", - "xrefs" : [ "GO:0003143" ] - }, { - "pred" : "hasExactSynonym", - "val" : "endocardial heart tube", - "xrefs" : [ "MP:0012700" ] + "val" : "mesoderm-derived epithelium" }, { "pred" : "hasExactSynonym", - "val" : "endocardial tube", - "xrefs" : [ "XAO:0000337" ] + "val" : "mesoepithelium" } ], "xrefs" : [ { - "val" : "AAO:0010411" - }, { - "val" : "EFO:0003526" - }, { - "val" : "EMAPA:32685" - }, { - "val" : "NCIT:C34161" - }, { - "val" : "TAO:0000360" - }, { - "val" : "XAO:0000337" - }, { - "val" : "ZFA:0000360" + "val" : "FMA:86452" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27770,26 +28042,22 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004151", - "lbl" : "cardiac chamber", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012292", + "lbl" : "embryonic cloacal fold", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cardiac chamber surrounds an enclosed cavity within the heart.", - "xrefs" : [ "GO:0003205" ] + "val" : "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly.", + "xrefs" : [ "MP:0011836", "MP:anna" ] }, - "comments" : [ "generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus" ], + "comments" : [ "We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "chamber of heart" - }, { - "pred" : "hasExactSynonym", - "val" : "heart chamber" + "pred" : "hasBroadSynonym", + "val" : "cloacal fold", + "xrefs" : [ "EHDAA2:0004009" ] } ], "xrefs" : [ { - "val" : "FMA:7095" - }, { - "val" : "SCTID:276456008" + "val" : "EHDAA2:0004009" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27797,30 +28065,68 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004176", - "lbl" : "external genitalia", + "id" : "http://purl.obolibrary.org/obo/UBERON_0012361", + "lbl" : "internal anal region", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EHDAA2:0004588" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0012469", + "lbl" : "external anal region", + "type" : "CLASS", + "meta" : { + "xrefs" : [ { + "val" : "EHDAA2:0004589" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0012476", + "lbl" : "skeleton of pelvic complex", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The external genitalia are the outer sex organs, such as the penis or vulva in mammals.", - "xrefs" : [ "GO:0035261" ] + "val" : "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "comments" : [ "TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "external genitalia" + "pred" : "hasRelatedSynonym", + "val" : "bones of lower limb", + "xrefs" : [ "FMA:24140" ] }, { "pred" : "hasRelatedSynonym", - "val" : "external reproductive organ" + "val" : "lower limb skeleton", + "xrefs" : [ "FMA:24140" ] }, { "pred" : "hasRelatedSynonym", - "val" : "external sex organ" + "val" : "ossa membri inferioris", + "xrefs" : [ "FMA:TA" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "pelvic complex skeleton", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "set of bones of lower limb", + "xrefs" : [ "FMA:24140" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "skeleton of posterior limb/fin and girdle", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "xrefs" : [ { - "val" : "FMA:45643" - }, { - "val" : "SCTID:362207005" + "val" : "FMA:24140" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27828,109 +28134,117 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004188", - "lbl" : "glomerular epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013241", + "lbl" : "embryonic urethral groove", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros.", - "xrefs" : [ "GO:0072010" ] + "val" : "The precursor of the urethra.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "epithelium of glomerulus" - }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of kidney glomerulus" + "val" : "sulcus urethralis primarius", + "xrefs" : [ "Wikipedia:Urethral_groove" ] }, { "pred" : "hasExactSynonym", - "val" : "epithelium of renal glomerulus" + "val" : "urethral groove" }, { "pred" : "hasExactSynonym", - "val" : "kidney glomerular epithelium", - "xrefs" : [ "MA:0002847" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "glomerular epithelial cell", - "xrefs" : [ "BTO:0001515" ] + "val" : "urethral sulcus" } ], "xrefs" : [ { - "val" : "BTO:0001515" - }, { - "val" : "EMAPA:35458" + "val" : "SCTID:361531004" }, { - "val" : "MA:0002847" + "val" : "Wikipedia:Urethral_groove" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - check - GO says outer, BTO says inner. Make this a superclass" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004190", - "lbl" : "renal glomerulus vasculature", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", + "lbl" : "subdivision of tube", + "type" : "CLASS", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013686", + "lbl" : "anatomical conduit space", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus.", - "xrefs" : [ "GO:0072012" ] + "val" : "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].", + "xrefs" : [ "FMA:9338", "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "glomerulus vasculature", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus vascular network", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus vasculature", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "vascular network of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "vasculature of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasNarrowSynonym", + "val" : "foramen space" + } ], + "xrefs" : [ { + "val" : "FMA:9338" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004198", - "lbl" : "comma-shaped body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", + "lbl" : "main body axis", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron.", - "xrefs" : [ "GO:0072049" ] + "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", + "lbl" : "body proper", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The region of the organism associated with the visceral organs.", + "xrefs" : [ "AEO:0000103" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", - "pred" : "hasExactSynonym", - "val" : "CSB" + "pred" : "hasRelatedSynonym", + "val" : "body", + "xrefs" : [ "AEO:0000103" ] + }, { + "pred" : "hasRelatedSynonym", + "val" : "whole body", + "xrefs" : [ "BTO:0001489" ] } ], "xrefs" : [ { - "val" : "EMAPA:27681" + "val" : "AEO:0000103" }, { - "val" : "ZFA:0005588" + "val" : "BTO:0001489" + }, { + "val" : "FMA:231424" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -27938,183 +28252,92 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004199", - "lbl" : "S-shaped body", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013756", + "lbl" : "venous blood", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron.", - "xrefs" : [ "GO:0072050" ] + "val" : "A blood that is part of a vein.", + "xrefs" : [ "OBOL:automatic" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", "pred" : "hasExactSynonym", - "val" : "SSB" + "val" : "blood in vein", + "xrefs" : [ "FMA:83067" ] }, { "pred" : "hasExactSynonym", - "val" : "stage II nephron", - "xrefs" : [ "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] + "val" : "portion of venous blood", + "xrefs" : [ "FMA:83067" ] + }, { + "pred" : "hasExactSynonym", + "val" : "venous blood", + "xrefs" : [ "FMA:83067" ] } ], "xrefs" : [ { - "val" : "EMAPA:27756" - }, { - "val" : "ZFA:0005589" + "val" : "FMA:83067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004200", - "lbl" : "kidney pyramid", + "id" : "http://purl.obolibrary.org/obo/UBERON_0013768", + "lbl" : "great vessel of heart", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts.", - "xrefs" : [ "GO:0072056", "http://anatomy.uams.edu/anatomyhtml/kidney.html" ] + "val" : "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.", + "xrefs" : [ "Wikipedia:Great_vessels" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "Groupings may vary - typically pulmonary vessels and aorta and vena cavae" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { "pred" : "hasBroadSynonym", - "val" : "pyramid", - "xrefs" : [ "GO:0072056" ] - }, { - "pred" : "hasExactSynonym", - "val" : "Malpighian pyramid", - "xrefs" : [ "Wikipedia:Renal_pyramids" ] + "val" : "great vessel" }, { "pred" : "hasExactSynonym", - "val" : "renal pyramid", - "xrefs" : [ "Wikipedia:Renal_pyramids" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", - "pred" : "hasRelatedSynonym", - "val" : "Malphigian pyramid", - "xrefs" : [ "BTO:0003926" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "Malpighian pyramid" - }, { - "pred" : "hasRelatedSynonym", - "val" : "medullary pyramid" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", - "pred" : "hasRelatedSynonym", - "val" : "pyramid of Malphigi", - "xrefs" : [ "ncithesaurus:Pyramid_of_Malpighi" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pyramid of Malpighi", - "xrefs" : [ "UBERON:cjm" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "pyramides renales", - "xrefs" : [ "Wikipedia:Renal_pyramids" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pyramis renalis", - "xrefs" : [ "BTO:0003926" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "renal medullary region", - "xrefs" : [ "FMA:258870" ] + "val" : "great vessel of thorax" } ], - "xrefs" : [ { - "val" : "BTO:0003926" - }, { - "val" : "FMA:258870" - }, { - "val" : "MA:0001654" - }, { - "val" : "NCIT:C12886" - }, { - "val" : "NCIT:C33436" - }, { - "val" : "SCTID:361328001" - }, { - "val" : "UMLS:C0227629" + "xrefs" : [ { + "val" : "EMAPA:36460" }, { - "val" : "UMLS:C1514613" + "val" : "SCTID:304066000" }, { - "val" : "Wikipedia:Renal_pyramids" + "val" : "Wikipedia:Great_vessels" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0002449" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005098" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" - }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004202", - "lbl" : "kidney outer medulla outer stripe", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", + "lbl" : "thoracic skeleton", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules.", - "xrefs" : [ "GO:0072058" ] + "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", + "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "outer medulla outer stripe", - "xrefs" : [ "MA:0002629" ] - }, { - "pred" : "hasExactSynonym", - "val" : "outer stripe", - "xrefs" : [ "GO:0072058" ] - }, { - "pred" : "hasExactSynonym", - "val" : "outer stripe of medulla of kidney", - "xrefs" : [ "FMA:76662" ] - }, { - "pred" : "hasExactSynonym", - "val" : "outer stripe of outer medulla", - "xrefs" : [ "EMAPA:29663" ] + "val" : "skeleton of thorax" }, { "pred" : "hasExactSynonym", - "val" : "outer stripe of renal medulla", - "xrefs" : [ "FMA:76662" ] + "val" : "thoracic part of axial skeleton" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", "pred" : "hasExactSynonym", - "val" : "stria externa medullae renalis", - "xrefs" : [ "FMA:76662", "FMA:TA" ] + "val" : "thoracic skeleton", + "xrefs" : [ "EHDAA2:0002013" ] } ], "xrefs" : [ { - "val" : "EMAPA:29663" + "val" : "EHDAA2:0002013" }, { - "val" : "FMA:76662" + "val" : "FMA:77169" }, { - "val" : "MA:0002629" + "val" : "Wikipedia:Thoracic_skeleton" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -28125,23 +28348,20 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004208", - "lbl" : "nephrogenic mesenchyme", + "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", + "lbl" : "primordial vasculature", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron.", - "xrefs" : [ "GO:0072076" ] + "val" : "A portion of tissue that will develop into vasculature.", + "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] }, - "comments" : [ "The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesenchyme of nephron", - "xrefs" : [ "OBOL:automatic" ] + "xrefs" : [ { + "val" : "EFO:0003708" }, { - "pred" : "hasExactSynonym", - "val" : "nephron mesenchyme", - "xrefs" : [ "OBOL:automatic" ] + "val" : "TAO:0005076" + }, { + "val" : "ZFA:0005076" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28149,48 +28369,45 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004209", - "lbl" : "renal vesicle", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", + "lbl" : "lateral structure", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells.", - "xrefs" : [ "GO:0072077" ] + "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "stage I nephron", - "xrefs" : [ "ZFA:0005586", "http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004211", - "lbl" : "nephron epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", + "lbl" : "circulatory organ", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The nephron epithelium is a tissue that covers the surface of a nephron.", - "xrefs" : [ "GO:0072088" ] + "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "epithelial tissue of nephron", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "hasBroadSynonym", + "val" : "heart" }, { "pred" : "hasExactSynonym", - "val" : "epithelium of nephron", - "xrefs" : [ "OBOL:automatic" ] + "val" : "cardiac pump" }, { "pred" : "hasExactSynonym", - "val" : "nephron epithelial tissue", - "xrefs" : [ "OBOL:automatic" ] + "val" : "heart or heart like organ" + }, { + "pred" : "hasNarrowSynonym", + "val" : "circulatory vessel" + }, { + "pred" : "hasRelatedSynonym", + "val" : "cardiac structure" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28198,64 +28415,20 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004212", - "lbl" : "glomerular capillary", + "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", + "lbl" : "heart plus pericardium", "type" : "CLASS", "meta" : { - "definition" : { - "val" : "The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus.", - "xrefs" : [ "MGI:csmith", "MP:0011320" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "blood capillary of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "capillary vessel of renal glomerulus", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus blood capillary", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus capillary", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal glomerulus capillary vessel", - "xrefs" : [ "OBOL:automatic" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "glomerular capillaries" - }, { - "pred" : "hasRelatedSynonym", - "val" : "glomerular capillary system", - "xrefs" : [ "MA:0002587" ] + "val" : "heart/pericardium", + "xrefs" : [ "MA:0002449" ] } ], "xrefs" : [ { - "val" : "EMAPA:28245" - }, { - "val" : "FMA:274259" - }, { - "val" : "MA:0002587" - }, { - "val" : "NCIT:C32684" - }, { - "val" : "SCTID:362049007" - }, { - "val" : "TAO:0005284" - }, { - "val" : "UMLS:C0226356" + "val" : "EMAPA:37597" }, { - "val" : "ZFA:0005284" + "val" : "MA:0002449" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -28266,86 +28439,95 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004288", - "lbl" : "skeleton", + "id" : "http://purl.obolibrary.org/obo/UBERON_0016566", + "lbl" : "pit", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.", - "xrefs" : [ "VSAO:0000026" ] + "val" : "An roughly circular indentation in a surface.", + "xrefs" : [ "AEO:0000204", "AEO:JB" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], + "xrefs" : [ { + "val" : "AEO:0000204" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", + "lbl" : "future central nervous system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Primordium that develops into the central nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "set of all bones" + "val" : "future CNS" }, { "pred" : "hasExactSynonym", - "val" : "set of bones of body" + "val" : "presumptive central nervous system" } ], - "xrefs" : [ { - "val" : "AEO:0000168" - }, { - "val" : "EHDAA2:0001843" - }, { - "val" : "EHDAA:5047" - }, { - "val" : "EMAPA:17213" - }, { - "val" : "FMA:23875" - }, { - "val" : "GAID:177" - }, { - "val" : "MA:0003006" - }, { - "val" : "MAT:0000032" - }, { - "val" : "MESH:D012863" - }, { - "val" : "MIAA:0000032" - }, { - "val" : "SCTID:361378004" - }, { - "val" : "VSAO:0000026" - }, { - "val" : "Wikipedia:Skeleton" - }, { - "val" : "XAO:0004053" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000469" }, { - "val" : "galen:Skeleton" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", + "lbl" : "future nervous system", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Primordium that develops into the nervous system.", + "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "presumptive nervous system", + "xrefs" : [ "AAO:0000477" ] + } ], + "xrefs" : [ { + "val" : "AAO:0000477" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "UBERON:3000477" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" } ] } }, { - 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The heart rudiment is the first structure of the heart tube.", - "xrefs" : [ "GO:0003313" ] + "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", + "xrefs" : [ "AEO:0000195", "AEO:JB" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "heart cone", - "xrefs" : [ "GO:0003313" ] + "val" : "extra-embryonic component" }, { "pred" : "hasExactSynonym", - "val" : "rudimentary heart", - "xrefs" : [ "ZFA:0000115" ] + "val" : "extraembryonic component", + "xrefs" : [ "AEO:0000195" ] } ], "xrefs" : [ { - "val" : "TAO:0000115" + "val" : "AEO:0000195" }, { - "val" : "ZFA:0000115" + "val" : "EHDAA2:0000003" + }, { + "val" : "EMAPA:16042" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -28353,4530 +28535,3603 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004341", - "lbl" : "primitive streak", + "id" : "http://purl.obolibrary.org/obo/UBERON_0018707", + "lbl" : "bladder organ", "type" : "CLASS", "meta" : { "definition" : { - 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The renal pelvis is the large cavity in the middle of each kidney. 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Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.", + "xrefs" : [ "Wikipedia:Microcirculation", "http://orcid.org/0000-0002-7073-9172" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "xrefs" : [ { - "val" : "AAO:0011129" - }, { - "val" : "TAO:0001890" - }, { - "val" : "VSAO:0000128" - }, { - "val" : "XAO:0004012" - }, { - "val" : "ZFA:0005494" + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "microvasculature" }, { - "val" : "galen:SkeletalStructure" + "pred" : "hasBroadSynonym", + "val" : "microvessel" } ], "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-2825-0621" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/2186" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "lbl" : "articular system", + "id" : "http://purl.obolibrary.org/obo/UBERON_8450002", + "lbl" : "excretory system", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all the joints of the body.", - "xrefs" : [ "VSAO:0000181" ] + "val" : "An anatomical system that eliminates waste products that arise as a result of metabolic activity.", + "xrefs" : [ "GO:0007588" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "joint system", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasExactSynonym", - "val" : "set of all joints of body", - "xrefs" : [ "FMA:23878" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of all joints" - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of joints of body", - "xrefs" : [ "FMA:23878" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:35150" - }, { - "val" : "FMA:23878" + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002175", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "val" : "MA:0003007" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "http://orcid.org/0000-0002-6095-8718" }, { - "val" : "SCTID:361827000" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2022-05-25T18:21:29Z" }, { - "val" : "VSAO:0000181" - } ], - "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004810", - "lbl" : "nephron tubule epithelium", + "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", + "lbl" : "visceral muscle tissue", "type" : "CLASS", "meta" : { "definition" : { - "val" : "The cellular avascular layer of the renal tubule luminar surfaces.", - "xrefs" : [ "MGI:csmith", "MP:0009640" ] + "val" : "A muscle tissue that is associated with soft internal organs (viscera).", + "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], + "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; 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Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { - "pred" : "hasExactSynonym", - "val" : "epithelium of kidney", - "xrefs" : [ "OBOL:automatic" ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. 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A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." }, { - "pred" : "hasRelatedSynonym", - "val" : "renal epithelium", - "xrefs" : [ "EMAPA:35457" ] - } ], - "xrefs" : [ { - "val" : "BTO:0000059" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "CALOHA:TS-0505" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "EMAPA:35457" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "part_of" }, { - "val" : "MA:0002846" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004852", - "lbl" : "cardiovascular system endothelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000051", + "lbl" : "has_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An endothelium that is part of the cardiovascular system.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a core relation that holds between a whole and its part" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "endothelia", - "xrefs" : [ "ZFA:0001639" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003004", - "pred" : "hasRelatedSynonym", - "val" : "vascular endothelia", - "xrefs" : [ "XAO:0000356" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "BTO:0001853" - }, { - "val" : "EMAPA:35201" - }, { - "val" : "GAID:519" - }, { - "val" : "MA:0000717" - }, { - "val" : "MESH:D004730" - }, { - "val" : "NCIT:C13053" + "val" : "BFO:0000051" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { - "val" : "TAO:0002171" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { - "val" : "UMLS:C0014261" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." }, { - "val" : "VHOG:0001217" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "val" : "XAO:0000356" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "quality" }, { - "val" : "ZFA:0001639" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_part" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/BFO_0000062", + "lbl" : "preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "xrefs" : [ { + "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider merging with 'endothelium'" + "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004872", - "lbl" : "splanchnic layer of lateral plate mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000063", + "lbl" : "precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].", - "xrefs" : [ "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" ] + "val" : "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "visceral mesoderm", - "xrefs" : [ "BILA:0000044", "http://www.drugs.com/dict/visceral-mesoderm.html", "http://www.stedmans.com/" ] - }, { - "pred" : "hasExactSynonym", - "val" : "inner layer of lateral plate mesoderm" - }, { - "pred" : "hasRelatedSynonym", - "val" : "splanchnic mesoderm", - "xrefs" : [ "ISBN:9780878932504" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AAO:0011102" - }, { - "val" : "BILA:0000044" - }, { - "val" : "FMA:295568" - }, { - "val" : "Wikipedia:Lateral_plate_mesoderm#Division_into_layers" - }, { - "val" : "XAO:0000276" + "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004874", - "lbl" : "somatopleure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000066", + "lbl" : "occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].", - "xrefs" : [ "Wikipedia:Somatopleure" ] + "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, + "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EHDAA2:0001847" - }, { - "val" : "EHDAA:381" - }, { - "val" : "EMAPA:16180" - }, { - "val" : "FMA:295566" - }, { - "val" : "NCIT:C34301" - }, { - "val" : "UMLS:C1519423" - }, { - "val" : "VHOG:0000557" - }, { - "val" : "Wikipedia:Somatopleure" + "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "occurs_in" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004875", - "lbl" : "nephrogenic cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/BFO_0000067", + "lbl" : "contains process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A portion of the urogenital ridge which is the source of much of the urinary system[WP].", - "xrefs" : [ "Wikipedia:Nephrogenic_cord" ] + "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "part_of or develops_from urogenital ridge?" ], - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "chorda nephrogenica", - "xrefs" : [ "Wikipedia:Nephrogenic_cord" ] - } ], + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030044", + "lbl" : "has_not_completed", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030045", + "lbl" : "lacks_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4030046", + "lbl" : "lacks_plasma_membrane_part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/GOREL_0002003", + "lbl" : "results_in_distribution_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "xrefs" : [ { - "val" : "FMA:72168" - }, { - "val" : "NCIT:C34219" - }, { - "val" : "SCTID:361405003" - }, { - "val" : "UMLS:C1283944" - }, { - "val" : "Wikipedia:Nephrogenic_cord" + "val" : "GOREL:0002003" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_distribution_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004876", - "lbl" : "urogenital fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/GOREL_0002004", + "lbl" : "results_in_fission_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].", - "xrefs" : [ "MP:0011835", "MP:anna", "Wikipedia:Urogenital_folds" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "urethral fold", - "xrefs" : [ "EMAPA:30888" ] - }, { - "pred" : "hasExactSynonym", - "val" : "urogenital fold", - "xrefs" : [ "EHDAA2:0004022", "MP:0011835" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", - "pred" : "hasRelatedSynonym", - "val" : "urogenital ridge", - "xrefs" : [ "MP:0011835" ] - } ], "xrefs" : [ { - "val" : "EHDAA2:0004022" - }, { - "val" : "EMAPA:30888" - }, { - "val" : "FMA:321919" - }, { - "val" : "Wikipedia:Urogenital_folds" + "val" : "GOREL:0002004" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_fission_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "lbl" : "chordamesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000052", + "lbl" : "characteristic of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The central region of trunk mesoderm. This tissue forms the notochord.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." + }, + "comments" : [ "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0000053", + "lbl" : "has characteristic", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Inverse of characteristic_of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "axial chorda mesoderm", - "xrefs" : [ "ZFA:0000091" ] - }, { - "pred" : "hasExactSynonym", - "val" : "chorda mesoderm" - }, { - "pred" : "hasExactSynonym", - "val" : "dorsal mesoderm", - "xrefs" : [ "https://github.com/obophenotype/uberon/wiki/The-neural-crest" ] - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive notochord", - "xrefs" : [ "ZFA:0000091" ] - } ], "xrefs" : [ { - "val" : "AAO:0000478" - }, { - "val" : "EFO:0003426" - }, { - "val" : "TAO:0000091" - }, { - "val" : "ZFA:0000091" + "val" : "RO:0000053" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bearer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004905", - "lbl" : "articulation", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000056", + "lbl" : "participates in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "joint" - } ], "xrefs" : [ { - "val" : "FBbt:00005811" + "val" : "RO:0000056" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "participates_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "lbl" : "subdivision of digestive tract", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000057", + "lbl" : "has participant", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A proximal-distal subdivision of the digestive tract.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "alimentary system subdivision", - "xrefs" : [ "FMA:71131" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "gut section", - "xrefs" : [ "FBbt:00100315" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "segment of intestinal tract" - }, { - "pred" : "hasRelatedSynonym", - "val" : "subdivision of alimentary system", - "xrefs" : [ "FMA:71131" ] - } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { - "val" : "FMA:71131" + "val" : "RO:0000057" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_participant" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "lbl" : "organ component layer", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000080", + "lbl" : "quality of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A part of a wall of an organ that forms a layer.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "FMA:82485" - } ], + "comments" : [ "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020." ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A quality inheres in its bearer at all times for which the quality exists." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005061", - "lbl" : "neural groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0000086", + "lbl" : "has quality", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.", - "xrefs" : [ "GO:0001842", "Wikipedia:Neural_groove", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, - "xrefs" : [ { - "val" : "AAO:0011071" - }, { - "val" : "EMAPA:35594" - }, { - "val" : "FMA:295624" - }, { - "val" : "NCIT:C34224" - }, { - "val" : "SCTID:361463007" - }, { - "val" : "UMLS:C0814992" - }, { - "val" : "Wikipedia:Neural_groove" - }, { - "val" : "XAO:0000248" - }, { - "val" : "neuronames:1363" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "lbl" : "neural fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001000", + "lbl" : "derives from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "One of the two elevated edges of the neural groove[GO,MP].", - "xrefs" : [ "GO:0001842", "MP:0011256", "Wikipedia:Neural_fold" ] + "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "medullary fold", - "xrefs" : [ "MP:0011256" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001249" - }, { - "val" : "FMA:295618" - }, { - "val" : "NCIT:C34223" - }, { - "val" : "SCTID:361461009" - }, { - "val" : "UMLS:C0814993" - }, { - "val" : "Wikipedia:Neural_fold" - }, { - "val" : "XAO:0004087" - }, { - "val" : "neuronames:1364" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005068", - "lbl" : "neural rod", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001001", + "lbl" : "derives into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].", - "xrefs" : [ "GO:0014024", "ZFA:0000133" ] + "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "neural tube rod", - "xrefs" : [ "GO:0014027" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003498" - }, { - "val" : "TAO:0000133" - }, { - "val" : "ZFA:0000133" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005080", - "lbl" : "metanephric ureteric bud", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001015", + "lbl" : "location of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].", - "xrefs" : [ "GO:0035502" ] + "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005081", - "lbl" : "ureter ureteric bud", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0001025", + "lbl" : "located in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].", - "xrefs" : [ "GO:0035503" ] + "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://wiki.geneontology.org/Located_in" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "lbl" : "muscle structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002000", + "lbl" : "2D boundary of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].", - "xrefs" : [ "GO:0061061" ] + "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "musculus", - "xrefs" : [ "FMA:30316" ] + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002002", + "lbl" : "has 2D boundary", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { - "pred" : "hasRelatedSynonym", - "val" : "muscle element" - } ], + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002005", + "lbl" : "innervated_by", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002006", + "lbl" : "has synaptic terminal of", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002007", + "lbl" : "bounding layer of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" + }, + "comments" : [ "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "FMA:30316" + "val" : "RO:0002007" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "bounding_layer_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005095", - "lbl" : "kidney rudiment", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002021", + "lbl" : "occurs across", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Missing definition for term UBERON:0005095. Please replace it using linked reference.", - "xrefs" : [ "GO:0072003" ] + "val" : "A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization." }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "kidney anlage", - "xrefs" : [ "GOC:mtg_kidney_jan10" ] - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "class added for consistency with GO - consider merging with kidney mesenchyme." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-7073-9172" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-20T17:19:37Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005096", - "lbl" : "descending thin limb", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002081", + "lbl" : "before or simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "Primitive instance level timing relation between events" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002082", + "lbl" : "simultaneous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO].", - "xrefs" : [ "GO:0072022", "Wikipedia:Descending_limb_of_loop_of_Henle" ] + "val" : "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "descending thin limb of loop of Henle" - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle descending thin limb" - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle thin descending limb", - "xrefs" : [ "MA:0002625" ] - }, { - "pred" : "hasExactSynonym", - "val" : "pars descendens (tubulus attenuatus)", - "xrefs" : [ "FMA:17719" ] - }, { - "pred" : "hasExactSynonym", - "val" : "thin descending limb" - }, { - "pred" : "hasRelatedSynonym", - "val" : "descending limb of Henle's loop", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "descending limb of loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "thin descending limb of loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "thin descending limb of the loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "thin descending loop of Henle", - "xrefs" : [ "Wikipedia:Descending_limb_of_loop_of_Henle" ] - } ], + "comments" : [ "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002086", + "lbl" : "ends after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002087", + "lbl" : "immediately preceded by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "xrefs" : [ { - "val" : "EMAPA:35514" - }, { - "val" : "FMA:17719" - }, { - "val" : "MA:0002625" - }, { - "val" : "Wikipedia:Descending_limb_of_loop_of_Henle" + "val" : "RO:0002087" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0005165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2276" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_preceded_by" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005097", - "lbl" : "renal connecting tubule", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002090", + "lbl" : "immediately precedes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO].", - "xrefs" : [ "GO:0072027", "Wikipedia:Connecting_tubule" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "connecting tubule", - "xrefs" : [ "MA:0002610" ] - }, { - "pred" : "hasExactSynonym", - "val" : "kidney connecting tubule", - "xrefs" : [ "MA:0002610" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasRelatedSynonym", - "val" : "tubulus renalis arcuatus", - "xrefs" : [ "Wikipedia:Connecting_tubule" ] - } ], + "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "BTO:0004539" - }, { - "val" : "EMAPA:27758" - }, { - "val" : "EMAPA:27790" - }, { - "val" : "EMAPA:28011" - }, { - "val" : "MA:0002610" - }, { - "val" : "Wikipedia:Connecting_tubule" + "val" : "RO:0002090" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "immediately_precedes" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005103", - "lbl" : "mesonephric epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002100", + "lbl" : "has soma location", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelium that is part of a mesonephros [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Relation between a neuron and a material anatomical entity that its soma is part of." }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some ?Y)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005156", - "lbl" : "reproductive structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002101", + "lbl" : "fasciculates with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any anatomical structure that is part of the reproductive system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002102", + "lbl" : "axon synapses in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between a neuron and some structure its axon forms (chemical) synapses in." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "reproductive system element" - }, { - "pred" : "hasExactSynonym", - "val" : "reproductive system structure" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some (\n and some (\n and some (\n and some ?Y)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005157", - "lbl" : "epithelial fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002103", + "lbl" : "synapsed by", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelial sheet bent on a linear axis.", - "xrefs" : [ "GO:0060571" ] + "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005164", - "lbl" : "ascending limb of loop of Henle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002104", + "lbl" : "has plasma membrane part", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP].", - "xrefs" : [ "MP:0011342", "Wikipedia:Ascending_limb_of_loop_of_Henle" ] + "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "ascending limb" - }, { - "pred" : "hasExactSynonym", - "val" : "ascending limb of Henle's loop" - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle ascending limb", - "xrefs" : [ "MP:0011342" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "distal straight tubule" - } ], - "xrefs" : [ { - "val" : "EMAPA:35510" - }, { - "val" : "FMA:17717" - }, { - "val" : "MA:0001676" - }, { - "val" : "NCIT:C32154" - }, { - "val" : "SCTID:245434005" - }, { - "val" : "UMLS:C0227658" - }, { - "val" : "Wikipedia:Ascending_limb_of_loop_of_Henle" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( and some ?Y)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005167", - "lbl" : "papillary duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002110", + "lbl" : "has postsynaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx.", - "xrefs" : [ "http://encyclopedia.thefreedictionary.com/" ] + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "papillary duct" - }, { - "pred" : "hasExactSynonym", - "val" : "papillary duct of kidney" - }, { - "pred" : "hasExactSynonym", - "val" : "renal papillary duct" - }, { - "pred" : "hasRelatedSynonym", - "val" : "Bellini's duct", - "xrefs" : [ "MP:0011331" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "duct of Bellini" - } ], - "xrefs" : [ { - "val" : "BTO:0004540" - }, { - "val" : "EMAPA:35655" - }, { - "val" : "MA:0001646" - }, { - "val" : "SCTID:110623009" - }, { - "val" : "Wikipedia:Duct_of_Bellini" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005169", - "lbl" : "interstitial tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002113", + "lbl" : "has presynaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Connective tissue between the cellular elements of a structure.", - "xrefs" : [ "http://medical-dictionary.thefreedictionary.com/tissue" ] + "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "interstitium" - } ], - "xrefs" : [ { - "val" : "FMA:86301" - }, { - "val" : "SCTID:85293002" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "specify differentia from stroma" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005172", - "lbl" : "abdomen element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002120", + "lbl" : "synapsed to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "abdomen organ", - "xrefs" : [ "MA:0000522" ] - } ], - "xrefs" : [ { - "val" : "MA:0000522" - }, { - "val" : "SCTID:272631008" - } ], + "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that part_of some ( that some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005173", - "lbl" : "abdominal segment element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002130", + "lbl" : "has synaptic terminal in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "abdominal segment organ", - "xrefs" : [ "MA:0000529" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37062" - }, { - "val" : "MA:0000529" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that some Y?)" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005177", - "lbl" : "trunk region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002131", + "lbl" : "overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trunk organ", - "xrefs" : [ "MA:0000516" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "EMAPA:37270" - }, { - "val" : "MA:0000516" + "val" : "RO:0002131" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "overlaps" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005178", - "lbl" : "thoracic cavity element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002132", + "lbl" : "has fasciculating neuron projection", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002134", + "lbl" : "innervates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "thoracic cavity organ", - "xrefs" : [ "MA:0000557" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37273" - }, { - "val" : "MA:0000557" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : " some ( that ( some ( that some Y?)))" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005179", - "lbl" : "pelvic region element", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002150", + "lbl" : "continuous with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." + }, + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "FMA:85972" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002158", + "lbl" : "shares ancestor with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." + }, + "comments" : [ "VBO calls this homologous_to" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002160", + "lbl" : "only in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pelvic element" - }, { - "pred" : "hasExactSynonym", - "val" : "pelvis organ", - "xrefs" : [ "MA:0000543" ] - }, { - "pred" : "hasExactSynonym", - "val" : "pelvis region organ" - } ], - "xrefs" : [ { - "val" : "EMAPA:37275" - }, { - "val" : "MA:0000543" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005181", - "lbl" : "thoracic segment organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002162", + "lbl" : "in taxon", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "upper body organ", - "xrefs" : [ "MA:0000563" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37271" - }, { - "val" : "MA:0000563" - } ], + "comments" : [ "Connects a biological entity to its taxon of origin." ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005185", - "lbl" : "renal medulla collecting duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002163", + "lbl" : "spatially disjoint from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The portion of the collecting duct that resides in the renal medulla.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A is spatially_disjoint_from B if and only if they have no parts in common" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "kidney medulla collecting duct", - "xrefs" : [ "MA:0002935" ] - }, { - "pred" : "hasExactSynonym", - "val" : "medullary collecting duct", - "xrefs" : [ "EMAPA:28061" ] - } ], - "xrefs" : [ { - "val" : "BTO:0004536" - }, { - "val" : "EMAPA:28061" + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " }, { - "val" : "EMAPA:35459" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", + "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" }, { - "val" : "MA:0002935" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005215", - "lbl" : "kidney interstitium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002170", + "lbl" : "connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes.", - "xrefs" : [ "DOI:10.1038/ki.1991.49", "PMID:18575881", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "interstitial tissue of kidney" - }, { - "pred" : "hasExactSynonym", - "val" : "renal interstitial tissue" - }, { - "pred" : "hasExactSynonym", - "val" : "renal interstitium", - "xrefs" : [ "FMA:70983" ] - }, { - "pred" : "hasExactSynonym", - "val" : "renal stroma", - "xrefs" : [ "FMA:70983" ] - }, { - "pred" : "hasExactSynonym", - "val" : "stroma of kidney", - "xrefs" : [ "FMA:70983" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "kidney interstitium group", - "xrefs" : [ "EMAPA:28518" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:28518" - }, { - "val" : "FMA:70983" - }, { - "val" : "MA:0002616" - }, { - "val" : "NCIT:C33459" - }, { - "val" : "SCTID:362210003" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005256", - "lbl" : "trunk mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002176", + "lbl" : "connects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Mesenchyme that is part of a developing trunk.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "trunk and cervical mesenchyme", - "xrefs" : [ "EHDAA2:0002092" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003485" - }, { - "val" : "EHDAA2:0002092" - }, { - "val" : "EHDAA:377" - }, { - "val" : "EMAPA:16177" - }, { - "val" : "TAO:0000081" - }, { - "val" : "VHOG:0000281" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { - "val" : "ZFA:0000081" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002177", + "lbl" : "attached to part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002178", + "lbl" : "supplies", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005291", - "lbl" : "embryonic tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002179", + "lbl" : "drains", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A portion of tissue that is part of an embryo.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "portion of embryonic tissue", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "developing tissue" - } ], - "xrefs" : [ { - "val" : "CALOHA:TS-2100" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005423", - "lbl" : "developing anatomical structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002180", + "lbl" : "has component", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "developing structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "developmental structure" - }, { - "pred" : "hasRelatedSynonym", - "val" : "developmental tissue", - "xrefs" : [ "MIAA:0000019" ] - } ], + "definition" : { + "val" : "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "xrefs" : [ { - "val" : "AEO:0000125" - }, { - "val" : "CALOHA:TS-2122" - }, { - "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" - }, { - "val" : "FMA:292313" - }, { - "val" : "MIAA:0000019" + "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "external" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_component" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005498", - "lbl" : "primitive heart tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002202", + "lbl" : "develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Multi-tissue structure that arises from the heart rudiment and will become the heart tube.", - "xrefs" : [ "ZFA:0000149" ] + "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive heart tube", - "xrefs" : [ "EMAPA:16215" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "early primitive heart tube", - "xrefs" : [ "EMAPA:16208" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0001512" - }, { - "val" : "EHDAA:424" - }, { - "val" : "EHDAA:436" - }, { - "val" : "EMAPA:16215" - }, { - "val" : "FMA:321916" - }, { - "val" : "SCTID:361522004" - }, { - "val" : "TAO:0000149" - }, { - "val" : "Wikipedia:Primitive_heart_tube" - }, { - "val" : "ZFA:0000149" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005564", - "lbl" : "gonad primordium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002203", + "lbl" : "develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Portion of tissue that gives rise to the immature gonad.", - "xrefs" : [ "ZFA:0001262" ] + "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future gonad", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "gonadal primordium", - "xrefs" : [ "ZFA:0001262" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primitive gonad", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "undifferentiated gonad", - "xrefs" : [ "ZFA:0001262" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "immature gonad", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - } ], - "xrefs" : [ { - "val" : "EFO:0003651" - }, { - "val" : "EHDAA:5927" - }, { - "val" : "EMAPA:17204" - }, { - "val" : "RETIRED_EHDAA2:0002148" - }, { - "val" : "TAO:0001262" - }, { - "val" : "WBbt:0008366" - }, { - "val" : "ZFA:0001262" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005721", - "lbl" : "pronephric mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002206", + "lbl" : "expressed in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A mesoderm that has the potential to develop into a pronephros.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002207", + "lbl" : "directly develops from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." }, - "comments" : [ "the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 \"Developmental Biology\", PMID:10720431 \"Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm\"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim" ], + "comments" : [ "TODO - add child relations from DOS" ], "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "pronephric anlage", - "xrefs" : [ "XAO:0000264" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pronephric bulge", - "xrefs" : [ "XAO:0000264" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pronephric mesenchyme", - "xrefs" : [ "XAO:0000264" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pronephric primordium", - "xrefs" : [ "XAO:0000264" ] - } ], - "xrefs" : [ { - "val" : "AAO:0011090" - }, { - "val" : "EFO:0003479" - }, { - "val" : "TAO:0000067" - }, { - "val" : "VHOG:0001239" - }, { - "val" : "XAO:0000264" - }, { - "val" : "ZFA:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "hasExactSynonym", + "val" : "has developmental precursor" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005749", - "lbl" : "glomerular tuft", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002210", + "lbl" : "directly develops into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The capillary loops of the kidney that normally function as a filtration unit[MP].", - "xrefs" : [ "MP:0005325", "Wikipedia:Glomerulus", "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "glomerular capillary tuft" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", - "pred" : "hasRelatedSynonym", - "val" : "glomerulus", - "xrefs" : [ "EMAPA:28239" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:28239" - }, { - "val" : "Wikipedia:Glomerulus" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005753", - "lbl" : "caudal part of nephrogenic cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002211", + "lbl" : "regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.", - "xrefs" : [ "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + "val" : "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "caudal portion of nephrogenic cord", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "caudal region of nephrogenic cord", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rear part of nephrogenic cord", - "xrefs" : [ "OBOL:automatic" ] - }, { - "pred" : "hasExactSynonym", - "val" : "rear portion of nephrogenic cord", - "xrefs" : [ "Wikipedia:Metanephros#Metanephros" ] + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002211" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005754", - "lbl" : "rostral part of nephrogenic cord", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002212", + "lbl" : "negatively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.", - "xrefs" : [ "http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron" ] + "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], + "xrefs" : [ { + "val" : "RO:0002212" + } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0004050", + "val" : "http://purl.obolibrary.org/obo/RO_0002211" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "negatively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005764", - "lbl" : "acellular membrane", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002213", + "lbl" : "positively regulates", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An acellular anatomical structure that is the bounding layer of a anatomical structure.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "FMA:63871" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { + "val" : "RO:0002213" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "positively_regulates" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "lbl" : "basement membrane of epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002215", + "lbl" : "capable of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.", - "xrefs" : [ "Wikipedia:Basement_membrane", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. 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If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. 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"id" : "http://purl.obolibrary.org/obo/UBERON_0007798", - "lbl" : "vascular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002410", + "lbl" : "causally related to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Anatomical system that consists of all blood and lymph vessels.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.", + "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "xrefs" : [ { - "val" : "BTO:0001085" - }, { - "val" : "CALOHA:TS-2053" - 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It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. 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Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007823", - "lbl" : "appendage girdle region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002411", + "lbl" : "causally upstream of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).", - "xrefs" : [ "UBERONREF:0000003", "https://orcid.org/0000-0002-6601-2165" ] + "val" : "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "girdle" - }, { - "pred" : "hasBroadSynonym", - "val" : "girdle region" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "fin girdle" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "fin girdle region" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "limb girdle" - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", - "pred" : "hasRelatedSynonym", - "val" : "limb girdle region" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "xrefs" : [ { - "val" : "EMAPA:37854" - }, { - "val" : "FMA:24874" - }, { - "val" : "VSAO:0000303" + "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0007824" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0007832", - "lbl" : "pelvic girdle skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002418", + "lbl" : "causally upstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.", - "xrefs" : [ "VSAO:0000155", "Wikipedia:Pelvis" ] + "val" : "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "pelvic girdle skeleton", - "xrefs" : [ "VSAO:0000155" ] - }, { - "pred" : "hasExactSynonym", - "val" : "skeletal parts of pelvic girdle", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "skeleton of pelvic girdle", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "synonymType" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", "pred" : "hasRelatedSynonym", - "val" : "pelvic girdle", - "xrefs" : [ "VSAO:0000155" ] + "val" : "affects" } ], "xrefs" : [ { - "val" : "AAO:0000426" - }, { - "val" : "AAO:0000768" - }, { - "val" : "EFO:0000947" - }, { - "val" : "EHDAA2:0001426" - }, { - "val" : "EHDAA:7149" - }, { - "val" : "EHDAA:8324" - }, { - "val" : "EMAPA:18028" - }, { - "val" : "FMA:87592" - }, { - "val" : "MAT:0000182" - }, { - "val" : "MIAA:0000182" - }, { - "val" : "TAO:0000565" - }, { - "val" : "VHOG:0000305" - }, { - "val" : "VSAO:0000155" - }, { - "val" : "Wikipedia:Pelvis" - }, { - "val" : "XAO:0003064" - }, { - "val" : "ZFA:0000565" - }, { - "val" : "galen:PelvicGirdle" - }, { - "val" : "http://people.eku.edu/ritchisong/pectoralgirdles.gif" + "val" : "RO:0002418" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" + "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" }, { - "pred" : "http://xmlns.com/foaf/0.1/depiction", - "val" : "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_upstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0008987", - "lbl" : "renal parenchyma", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002427", + "lbl" : "causally downstream of or within", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The functional tissue of the kidney, consisting of the nephrons.", - "xrefs" : [ "BTO:0003604" ] + "val" : "inverse of causally upstream of or within" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "parenchyma of kidney", - "xrefs" : [ "FMA:15574" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "kidney parenchyma", - "xrefs" : [ "BTO:0003604" ] - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "xrefs" : [ { - "val" : "BTO:0003604" - }, { - "val" : "FMA:15574" - }, { - "val" : "SCTID:29704000" + "val" : "RO:0002427" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "causally_downstream_of_or_within" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009035", - "lbl" : "renal straight tubule", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002428", + "lbl" : "involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002431", + "lbl" : "involved in or involved in regulation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "kidney straight tubule", - "xrefs" : [ "MA:0002634" ] - }, { - "pred" : "hasExactSynonym", - "val" : "straight tubule" - } ], - "xrefs" : [ { - "val" : "EMAPA:37489" - }, { - "val" : "MA:0002634" - }, { - "val" : "SCTID:245151008" - }, { - "val" : "Wikipedia:Tubuli_seminiferi_recti" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "OWL does not allow defining object properties via a Union" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009142", - "lbl" : "entire embryonic mesenchyme", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002433", + "lbl" : "contributes to morphology of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Sum total of mesenchyme in the embryo.", - "xrefs" : [ "https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7" ] + "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002473", + "lbl" : "composed primarily of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "xrefs" : [ { - "val" : "EHDAA2:0001113" - }, { - "val" : "EHDAA:177" - }, { - "val" : "EMAPA:16097" - } ], + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002479", + "lbl" : "has part that occurs in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002485", + "lbl" : "receives input from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:0003313" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "See notes for inverse relation" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009196", - "lbl" : "indifferent external genitalia", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002486", + "lbl" : "sends output to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#organ_slim" ], - "xrefs" : [ { - "val" : "EHDAA2:0004021" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009201", - "lbl" : "nephric duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002487", + "lbl" : "relation between physical entity and a process or stage", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002488", + "lbl" : "existence starts during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A nephric duct is a tube that drains a primitive kidney[GO].", - "xrefs" : [ "GO:0072176" ] + "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002489", + "lbl" : "existence starts with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002490", + "lbl" : "existence overlaps", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "pronephric duct or mesonephric duct" ], - "xrefs" : [ { - "val" : "EMAPA:16577" - }, { - "val" : "Wikipedia:Wolffian_duct" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009569", - "lbl" : "subdivision of trunk", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002491", + "lbl" : "existence starts and ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "definition" : { + "val" : "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "region of trunk", - "xrefs" : [ "FMA:25054" ] - }, { - "pred" : "hasExactSynonym", - "val" : "trunk subdivision", - "xrefs" : [ "FMA:25054" ] - } ], - "xrefs" : [ { - "val" : "FMA:25054" - }, { - "val" : "SCTID:22943007" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "exists during" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "lbl" : "trunk paraxial mesoderm", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002492", + "lbl" : "existence ends during", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "trunk and cervical paraxial mesenchyme", - "xrefs" : [ "EHDAA2:0002094" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "trunk paraxial mesenchyme", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/30" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002094" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009773", - "lbl" : "renal tubule", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002493", + "lbl" : "existence ends with", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis.", - "xrefs" : [ "DOI:10.1371/journal.pone.0099864", "GO:0061333", "GOC:dph", "GOC:mtg_kidney_jan10" ] + "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "renal tubule (generic)", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasExactSynonym", - "val" : "tubule of excretory system", - "xrefs" : [ "OBOL:automatic", "https://orcid.org/0000-0002-6601-2165" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0009856", - "lbl" : "sac", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002494", + "lbl" : "transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002495", + "lbl" : "immediate transformation of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002496", + "lbl" : "existence starts during or after", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002497", + "lbl" : "existence ends during or before", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." + }, + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002500", + "lbl" : "causal agent in process", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002501", + "lbl" : "causal relation between processes", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002502", + "lbl" : "depends on", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - 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In vertebrates, this is based on the vertebral column.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "axial subdivision of organism" - }, { - "pred" : "hasRelatedSynonym", - "val" : "body segment" - }, { - "pred" : "hasRelatedSynonym", - "val" : "main body segment" + "val" : "has synaptic input or output in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-1373-1705" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-17T09:26:52Z" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0011695", - "lbl" : "embryonic cardiovascular system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0013007", + "lbl" : "has sensory dendrite in", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A cardiovascular system that is part of a conceptus.", - "xrefs" : [ "OBOL:automatic" ] + "val" : "Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite." }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "conceptus cardiovascular system" + "val" : "has sensory dendrite location" }, { - "pred" : "hasRelatedSynonym", - "val" : "embryonic circulatory system" + "pred" : "hasExactSynonym", + "val" : "has sensory terminal in" }, { - "pred" : "hasRelatedSynonym", - "val" : "fetal circulatory system" + "pred" : "hasExactSynonym", + "val" : "has sensory terminal location" } ], - "xrefs" : [ { - "val" : "EHDAA2:0000216" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-1373-1705" }, { - "val" : "FMA:305965" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2020-07-20T12:10:09Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015006", + "lbl" : "different in magnitude relative to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015007", + "lbl" : "increased in magnitude relative to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015008", + "lbl" : "decreased in magnitude relative to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015010", + "lbl" : "has relative magnitude", + "type" : "PROPERTY", + "propertyType" : "OBJECT" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015011", + "lbl" : "has cross section", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "comments" : [ "Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round." ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015015", + "lbl" : "has high plasma membrane amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1617-8244" }, { - "val" : "NCIT:C34148" - } ], + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1940-6740" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0015016", + "lbl" : "has low plasma membrane amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface.", + "xrefs" : [ "PMID:19243617" ] + }, "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1617-8244" + }, { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-1940-6740" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "lbl" : "coelom", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0017001", + "lbl" : "device utilizes material", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.", - "xrefs" : [ "UBERON:cjm", "Wikipedia:Body_cavity", "Wikipedia:Coelom" ] + "val" : "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." }, "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "enterocoelom", - "xrefs" : [ "NCBITaxon:33511" ] - }, { - "pred" : "hasNarrowSynonym", - "val" : "haemocoelom" - }, { - "pred" : "hasNarrowSynonym", - "val" : "schizocoelom" + "pred" : "hasBroadSynonym", + "val" : "utilizes" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-9625-1899" }, { - "pred" : "hasRelatedSynonym", - "val" : "coelem" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2620-0345" }, { - "pred" : "hasRelatedSynonym", - "val" : "coelomic cavity", - "xrefs" : [ "EHDAA2:0004731" ] - } ], + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2021-11-08T12:00:00Z" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0040036", + "lbl" : "results in changes to anatomical or cellular structure", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "p has anatomical participant c iff p has participant c, and c is an anatomical entity" + }, "xrefs" : [ { - "val" : "EHDAA2:0004731" - }, { - "val" : "Wikipedia:Coelom" + "val" : "RO:0040036" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-09-26T01:08:58Z" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "results_in_changes_to_anatomical_or_cellular_structure" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012274", - "lbl" : "columnar epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", + "lbl" : "obsolete has_high_plasma_membrane_amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified].", - "xrefs" : [ "Wikipedia:Columnar_epithelium" ] + "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", + "xrefs" : [ "PMID:19243617" ] }, - "xrefs" : [ { - "val" : "Wikipedia:Columnar_epithelium" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0015015" + } ], + "deprecated" : true } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012275", - "lbl" : "meso-epithelium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", + "lbl" : "obsolete has_low_plasma_membrane_amount", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Epithelium that derives from the mesoderm. [Automatically generated definition].", - "xrefs" : [ "OBOL:automatic" ] + "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", + "xrefs" : [ "PMID:19243617" ] }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "mesoderm-derived epithelium" + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" }, { - "pred" : "hasExactSynonym", - "val" : "mesoepithelium" - } ], - "xrefs" : [ { - "val" : "FMA:86452" + "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", + "val" : "http://purl.obolibrary.org/obo/RO_0015016" } ], + "deprecated" : true + } + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", + "lbl" : "anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "definition" : { + "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] + }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012292", - "lbl" : "embryonic cloacal fold", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "lbl" : "channel for", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly.", - "xrefs" : [ "MP:0011836", "MP:anna" ] - }, - "comments" : [ "We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts" ], "synonyms" : [ { "pred" : "hasBroadSynonym", - "val" : "cloacal fold", - "xrefs" : [ "EHDAA2:0004009" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0004009" + "val" : "carries" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -32884,303 +32139,164 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012361", - "lbl" : "internal anal region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", + "lbl" : "channels_from", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "EHDAA2:0004588" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012469", - "lbl" : "external anal region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", + "lbl" : "channels_into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "xrefs" : [ { - "val" : "EHDAA2:0004589" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0012476", - "lbl" : "skeleton of pelvic complex", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "lbl" : "distally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "bones of lower limb", - "xrefs" : [ "FMA:24140" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "lower limb skeleton", - "xrefs" : [ "FMA:24140" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "ossa membri inferioris", - "xrefs" : [ "FMA:TA" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "pelvic complex skeleton", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "set of bones of lower limb", - "xrefs" : [ "FMA:24140" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "skeleton of posterior limb/fin and girdle", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - } ], - "xrefs" : [ { - "val" : "FMA:24140" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013241", - "lbl" : "embryonic urethral groove", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", + "lbl" : "extends_fibers_into", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The precursor of the urethra.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, - "synonyms" : [ { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003011", - "pred" : "hasExactSynonym", - "val" : "sulcus urethralis primarius", - "xrefs" : [ "Wikipedia:Urethral_groove" ] - }, { - "pred" : "hasExactSynonym", - "val" : "urethral groove" - }, { - "pred" : "hasExactSynonym", - "val" : "urethral sulcus" - } ], - "xrefs" : [ { - "val" : "SCTID:361531004" - }, { - "val" : "Wikipedia:Urethral_groove" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013522", - "lbl" : "subdivision of tube", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", + "lbl" : "filtered through", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { + "definition" : { + "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." + }, + "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013686", - "lbl" : "anatomical conduit space", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", + "lbl" : "indirectly_supplies", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].", - "xrefs" : [ "FMA:9338", "http://orcid.org/0000-0002-6601-2165" ] + "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "foramen space" - } ], - "xrefs" : [ { - "val" : "FMA:9338" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "add to RO" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "lbl" : "main body axis", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", + "lbl" : "layer part of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013702", - "lbl" : "body proper", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", + "lbl" : "posteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "The region of the organism associated with the visceral organs.", - "xrefs" : [ "AEO:0000103" ] + "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "body", - "xrefs" : [ "AEO:0000103" ] - }, { - "pred" : "hasRelatedSynonym", - "val" : "whole body", - "xrefs" : [ "BTO:0001489" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000103" - }, { - "val" : "BTO:0001489" - }, { - "val" : "FMA:231424" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013756", - "lbl" : "venous blood", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", + "lbl" : "protects", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A blood that is part of a vein.", - "xrefs" : [ "OBOL:automatic" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "blood in vein", - "xrefs" : [ "FMA:83067" ] - }, { - "pred" : "hasExactSynonym", - "val" : "portion of venous blood", - "xrefs" : [ "FMA:83067" ] - }, { - "pred" : "hasExactSynonym", - "val" : "venous blood", - "xrefs" : [ "FMA:83067" ] - } ], - "xrefs" : [ { - "val" : "FMA:83067" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0013768", - "lbl" : "great vessel of heart", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", + "lbl" : "proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.", - "xrefs" : [ "Wikipedia:Great_vessels" ] + "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", + "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] }, - "comments" : [ "Groupings may vary - typically pulmonary vessels and aorta and vena cavae" ], - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "great vessel" - }, { - "pred" : "hasExactSynonym", - "val" : "great vessel of thorax" - } ], - "xrefs" : [ { - "val" : "EMAPA:36460" - }, { - "val" : "SCTID:304066000" - }, { - "val" : "Wikipedia:Great_vessels" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014477", - "lbl" : "thoracic skeleton", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", + "lbl" : "sexually_homologous_to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.", - "xrefs" : [ "Wikipedia:Rib_cage", "https://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "skeleton of thorax" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic part of axial skeleton" - }, { - "pred" : "hasExactSynonym", - "val" : "thoracic skeleton", - "xrefs" : [ "EHDAA2:0002013" ] - } ], - "xrefs" : [ { - "val" : "EHDAA2:0002013" - }, { - "val" : "FMA:77169" - }, { - "val" : "Wikipedia:Thoracic_skeleton" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0014903", - "lbl" : "primordial vasculature", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", + "lbl" : "site_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "A portion of tissue that will develop into vasculature.", - "xrefs" : [ "ZFA:0005076", "ZFA:curator" ] + "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." }, - "xrefs" : [ { - "val" : "EFO:0003708" - }, { - "val" : "TAO:0005076" - }, { - "val" : "ZFA:0005076" + "synonyms" : [ { + "pred" : "hasRelatedSynonym", + "val" : "capable_of_has_part" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -33188,537 +32304,496 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "lbl" : "lateral structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", + "lbl" : "subdivision of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "Any structure that is placed on one side of the left-right axis of a bilaterian.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], + "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015228", - "lbl" : "circulatory organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", + "lbl" : "transitively anteriorly connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "definition" : { - "val" : "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "heart" - }, { - "pred" : "hasExactSynonym", - "val" : "cardiac pump" - }, { - "pred" : "hasExactSynonym", - "val" : "heart or heart like organ" - }, { - "pred" : "hasNarrowSynonym", - "val" : "circulatory vessel" - }, { - "pred" : "hasRelatedSynonym", - "val" : "cardiac structure" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" + }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0015410", - "lbl" : "heart plus pericardium", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", + "lbl" : "transitively distally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", "meta" : { - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "heart/pericardium", - "xrefs" : [ "MA:0002449" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:37597" + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { - "val" : "MA:0002449" - } ], + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", + "lbl" : "transitively proximally connected to", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", + "lbl" : "trunk_part_of", + "type" : "PROPERTY", + "propertyType" : "OBJECT", + "meta" : { + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016566", - "lbl" : "pit", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000002", + "lbl" : "example to be eventually removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000103", + "lbl" : "failed exploratory term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000120", + "lbl" : "metadata complete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000121", + "lbl" : "organizational term", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000122", + "lbl" : "ready for release", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000123", + "lbl" : "metadata incomplete", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000124", + "lbl" : "uncurated", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000125", + "lbl" : "pending final vetting", + "type" : "INDIVIDUAL", + "meta" : { + "definition" : { + "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." + } + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000226", + "lbl" : "placeholder removed", + "type" : "INDIVIDUAL" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000227", + "lbl" : "terms merged", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "An editor note should explain what were the merged terms and the reason for the merge." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000228", + "lbl" : "term imported", + "type" : "INDIVIDUAL", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000229", + "lbl" : "term split", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "An roughly circular indentation in a surface.", - "xrefs" : [ "AEO:0000204", "AEO:JB" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], - "xrefs" : [ { - "val" : "AEO:0000204" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016879", - "lbl" : "future central nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000410", + "lbl" : "universal", + "type" : "INDIVIDUAL", "meta" : { - "definition" : { - "val" : "Primordium that develops into the central nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "future CNS" - }, { - "pred" : "hasExactSynonym", - "val" : "presumptive central nervous system" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000469" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016880", - "lbl" : "future nervous system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000420", + "lbl" : "defined class", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Primordium that develops into the nervous system.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "presumptive nervous system", - "xrefs" : [ "AAO:0000477" ] - } ], - "xrefs" : [ { - "val" : "AAO:0000477" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", - "val" : "UBERON:3000477" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0016887", - "lbl" : "entire extraembryonic component", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000421", + "lbl" : "named class expression", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.", - "xrefs" : [ "AEO:0000195", "AEO:JB" ] + "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "extra-embryonic component" - }, { - "pred" : "hasExactSynonym", - "val" : "extraembryonic component", - "xrefs" : [ "AEO:0000195" ] - } ], - "xrefs" : [ { - "val" : "AEO:0000195" - }, { - "val" : "EHDAA2:0000003" - }, { - "val" : "EMAPA:16042" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0018707", - "lbl" : "bladder organ", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000423", + "lbl" : "to be replaced with external ontology term", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "A membranous sac in animals that serves as the receptacle of a liquid or contains gas.", - "xrefs" : [ "BTO:0000123" ] - }, - "synonyms" : [ { - "pred" : "hasNarrowSynonym", - "val" : "bladder", - "xrefs" : [ "BTO:0000123" ] - } ], - "xrefs" : [ { - "val" : "BTO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "Terms with this status should eventually replaced with a term from another ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034921", - "lbl" : "multi organ part structure", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000428", + "lbl" : "requires discussion", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "An multicellular anatomical structure that has subparts of multiple organs as a part.", - "xrefs" : [ "CARO:0020001" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "anatomical cluster", - "xrefs" : [ "CARO:0020001" ] - } ], - "xrefs" : [ { - "val" : "CARO:0020001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034923", - "lbl" : "disconnected anatomical group", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0001000", + "lbl" : "out of scope", + "type" : "INDIVIDUAL", "meta" : { "definition" : { - "val" : "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.", - "xrefs" : [ "CARO:0020000" ] + "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", + "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034925", - "lbl" : "anatomical collection", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000028", + "lbl" : "symbol", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/IAO_0000115", + "lbl" : "definition", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A collection of anatomical structures that are alike in terms of their morphology or developmental origin.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] + "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034969", - "lbl" : "epithelial layer of duct", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000116", + "lbl" : "editor note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "duct epithelium" - }, { - "pred" : "hasRelatedSynonym", - "val" : "ductal epithelium" - } ], - "xrefs" : [ { - "val" : "NCIT:C25787" - }, { - "val" : "UMLS:C1512086" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034996", - "lbl" : "outer renal medulla loop of Henle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000231", + "lbl" : "has obsolescence reason", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "loop of Henle, outer medullary portion", - "xrefs" : [ "EMAPA:28322" ] - } ], - "xrefs" : [ { - "val" : "EMAPA:28322" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "definition" : { + "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0034997", - "lbl" : "renal medulla loop of Henle", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000233", + "lbl" : "term tracker item", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "loop of Henle of renal medulla", - "xrefs" : [ "EMAPA:35460" ] - }, { - "pred" : "hasExactSynonym", - "val" : "loop of Henle, medullary portion" - } ], + "definition" : { + "val" : "An IRI or similar locator for a request or discussion of an ontology term." + }, + "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "xrefs" : [ { - "val" : "EMAPA:35460" + "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "term_tracker_item" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035554", - "lbl" : "right cardiac chamber", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000424", + "lbl" : "expand expression to", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Any chamber of the right side of the heart.", - "xrefs" : [ "http://orcid.org/0000-0002-6601-2165" ] - }, - "xrefs" : [ { - "val" : "FMA:7165" - }, { - "val" : "SCTID:362007002" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" + } } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0035804", - "lbl" : "future mouth", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0000700", + "lbl" : "preferred_root", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The primordial mouth region of the developing head.", - "xrefs" : [ "MP:0003119" ] + "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "primitive mouth", - "xrefs" : [ "FMA:293105" ] - }, { - "pred" : "hasExactSynonym", - "val" : "primordial mouth" - } ], "xrefs" : [ { - "val" : "FMA:293105" + "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "val" : "external" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "val" : "true" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", + "val" : "has_ontology_root_term" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036146", - "lbl" : "cardiopharyngeal field", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/IAO_0100001", + "lbl" : "term replaced by", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.", - "xrefs" : [ "http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1", "https://orcid.org/0000-0003-3308-6245" ] + "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036215", - "lbl" : "anatomical surface region", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0002000", + "lbl" : "defined by construct", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Material anatomical entity that forms the outermost boundary of an anatomical structure.", - "xrefs" : [ "https://github.com/obophenotype/uberon/issues/1324" ] + "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], - "xrefs" : [ { - "val" : "AAO:0010270" - }, { - "val" : "ZFA:0005594" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/ontodev/robot/issues/963" }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-7356-1779" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/elements/1.1/contributor", + "val" : "https://orcid.org/0000-0002-8688-6599" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_0036295", - "lbl" : "renal pelvis/ureter", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003000", + "lbl" : "abbreviation", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra.", - "xrefs" : [ "NCIT:C54419" ] + "val" : "A synonym type for describing abbreviations or initalisms" }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "renal pelvis and ureter" - }, { - "pred" : "hasExactSynonym", - "val" : "renal pelvis plus ureter" - } ], - "xrefs" : [ { - "val" : "NCIT:C54419" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8410081", - "lbl" : "blood microvessel", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003002", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003003", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/OMO_0003004", + "lbl" : "plural form", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins.", - "xrefs" : [ "Wikipedia:Microcirculation", "http://orcid.org/0000-0002-7073-9172" ] + "val" : "A synonym type for describing pluralization synonyms" }, - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "microvasculature" - }, { - "pred" : "hasBroadSynonym", - "val" : "microvessel" - } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-2825-0621" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/122" }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/2186" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-4423-4370" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8450002", - "lbl" : "excretory system", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/OMO_0003011", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002161", + "lbl" : "never in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "An anatomical system that eliminates waste products that arise as a result of metabolic activity.", - "xrefs" : [ "GO:0007588" ] + "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "val" : "http://orcid.org/0000-0002-6095-8718" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2022-05-25T18:21:29Z" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { - "id" : "http://purl.obolibrary.org/obo/UBERON_8600004", - "lbl" : "visceral muscle tissue", - "type" : "CLASS", + "id" : "http://purl.obolibrary.org/obo/RO_0002175", + "lbl" : "present in taxon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { - "val" : "A muscle tissue that is associated with soft internal organs (viscera).", - "xrefs" : [ "BTO:0002780", "CLAO:0001295" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, - "comments" : [ "It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "visceral muscle" - } ], + "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0001-6677-8489" + "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", + "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" }, { - "pred" : "http://purl.org/dc/terms/date", - "val" : "2023-02-16T10:17:46Z" + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002259", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0004050", + "lbl" : "is negative form of", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "https://orcid.org/0000-0002-6601-2165" }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-03-14T00:03:24Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_gp2term", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_go_ontology", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/valid_for_gocam", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#BDS_subset", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/cl#added_for_HCA", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim", "lbl" : "blood_and_immune_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin" ], "basicPropertyValues" : [ { @@ -33730,6 +32805,7 @@ "id" : "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "lbl" : "eye_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the eye." ] } @@ -33737,49 +32813,15 @@ "id" : "http://purl.obolibrary.org/obo/cl#general_cell_types_upper_slim", "lbl" : "general_cell_types_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes of cell types in the cell ontology." ] } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount", - "lbl" : "obsolete has_high_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015015" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount", - "lbl" : "obsolete has_low_plasma_membrane_amount", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "OBSOLETE A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).", - "xrefs" : [ "PMID:19243617" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", - "val" : "https://github.com/obophenotype/cell-ontology/issues/1481" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibrary.org/obo/RO_0015016" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/cl#kidney_upper_slim", "lbl" : "kidney_upper_slim", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "comments" : [ "a subset of general classes related to specific cell types in the kidney" ], "basicPropertyValues" : [ { @@ -33787,291 +32829,391 @@ "val" : "2023-11-22T11:18:57Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_candida", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_chembl", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_drosophila", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_euk_cellular_processes_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_generic", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_metagenomics", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_mouse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pir", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_pombe", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_prokaryote_ribbon", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_synapse", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#goslim_yeast", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#syngo_official_label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#systematic_synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#blast_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#equivalent_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#in_part", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#scientific_name", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ncbitaxon#synonym", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#abnormal_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#attribute_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#cell_quality", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#disposition_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#mpath_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#scalar_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pato#value_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#Gene-based", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/pr#PRO-short-label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ro/subsets#ro-eco", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#HUMAN_PREFERRED", "lbl" : "preferred term when talking about an instance of this class in Homo sapiens", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#LATIN", "lbl" : "latin term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon#PLURAL", "lbl" : "plural term", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#COMPARATIVE_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#DEPRECATED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HOMOLOGY", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#HUMAN_PREFERRED", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#INCONSISTENT", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/uberon/core#MISSPELLING", "lbl" : "a mis-spelling that is in common use and thus recorded", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "lbl" : "anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#NON_MAMMAL", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "lbl" : "channel for", + "id" : "http://purl.obolibrary.org/obo/uberon/core#PENDING_REVIEW", "type" : "PROPERTY", - "meta" : { - "synonyms" : [ { - "pred" : "hasBroadSynonym", - "val" : "carries" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", - "lbl" : "channels_from", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SENSU", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#channels_into", - "lbl" : "channels_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#SYSTEMATIC", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "lbl" : "distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#added_for_HCA", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "lbl" : "extends_fibers_into", + "id" : "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y", - "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#filtered_through", - "lbl" : "filtered through", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cumbo", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." - }, - "comments" : [ "Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "lbl" : "indirectly_supplies", + "id" : "http://purl.obolibrary.org/obo/uberon/core#cyclostome_subset", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "add to RO" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", - "lbl" : "layer part of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#developmental_classification", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "lbl" : "posteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#dubious_grouping", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#protects", - "lbl" : "protects", + "id" : "http://purl.obolibrary.org/obo/uberon/core#early_development", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "lbl" : "proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.", - "xrefs" : [ "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" ] - }, - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#sexually_homologous_to", - "lbl" : "sexually_homologous_to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#emapa_ehdaa2", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#site_of", - "lbl" : "site_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#functional_classification", "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." - }, - "synonyms" : [ { - "pred" : "hasRelatedSynonym", - "val" : "capable_of_has_part" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#subdivision_of", - "lbl" : "subdivision of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "type" : "PROPERTY", - "meta" : { - "comments" : [ "placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B" ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to", - "lbl" : "transitively anteriorly connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#homology_grouping", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to", - "lbl" : "transitively distally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] + "comments" : [ "" ] } }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to", - "lbl" : "transitively proximally connected to", + "id" : "http://purl.obolibrary.org/obo/uberon/core#inconsistent_with_fma", "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" - } ] - } + "propertyType" : "ANNOTATION" }, { - "id" : "http://purl.obolibrary.org/obo/uberon/core#trunk_part_of", - "lbl" : "trunk_part_of", + "id" : "http://purl.obolibrary.org/obo/uberon/core#location_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#major_organ", "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#non_informative", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#organ_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#phenotype_rcn", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#unverified_taxonomic_grouping", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/ubprop#_upper_level", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - } ] + "comments" : [ "abstract upper-level terms not directly useful for analysis" ] } + }, { + "id" : "http://purl.org/dc/elements/1.1/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/creator", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/elements/1.1/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/contributor", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/date", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/license", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/title", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty", "lbl" : "synonym_type_property", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#consider", "lbl" : "consider", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", "lbl" : "created by", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "lbl" : "creation date", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "lbl" : "has_alternative_id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym", "lbl" : "has_broad_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." @@ -34087,11 +33229,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref", "lbl" : "database_cross_reference", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym", "lbl" : "has_exact_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." @@ -34108,6 +33252,7 @@ "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym", "lbl" : "has_narrow_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." @@ -34123,11 +33268,13 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "lbl" : "has_obo_namespace", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym", "lbl" : "has_related_synonym", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "definition" : { "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." @@ -34143,23 +33290,52 @@ }, { "id" : "http://www.geneontology.org/formats/oboInOwl#hasSynonymType", "lbl" : "has_synonym_type", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", "lbl" : "id", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset", "lbl" : "in_subset", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#note", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "lbl" : "shorthand", - "type" : "PROPERTY" + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.geneontology.org/formats/oboInOwl#source", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#comment", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://www.w3.org/2000/01/rdf-schema#label", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "lbl" : "see also", "type" : "PROPERTY", + "propertyType" : "ANNOTATION", "meta" : { "xrefs" : [ { "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" @@ -34169,6 +33345,18 @@ "val" : "seeAlso" } ] } + }, { + "id" : "http://www.w3.org/2002/07/owl#deprecated", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "http://xmlns.com/foaf/0.1/depiction", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" + }, { + "id" : "https://w3id.org/sssom/mapping_justification", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -34352,14 +33540,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000134" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000064", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000064", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/GO_0005929" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", @@ -34368,14 +33548,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000483" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000067", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000064" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000067", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000066" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000068", "pred" : "is_a", @@ -34384,16 +33556,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000068", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000058" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000076", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "is_a", @@ -34442,8 +33604,8 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000213" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + "pred" : "http://purl.obolibrary.org/obo/RO_0002202", + "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000133", "pred" : "is_a", @@ -34584,14 +33746,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000232", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000558" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000239", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000067" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000239", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000075" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", "pred" : "is_a", @@ -35061,7 +34215,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000666", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + "obj" : "http://purl.obolibrary.org/obo/CL_0000115" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000666", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/PATO_0002064" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000669", "pred" : "is_a", @@ -35349,21 +34507,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000115", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000666" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000666" + "obj" : "http://purl.obolibrary.org/obo/CL_0002681" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_1000746" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000074" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002242", "pred" : "is_a", @@ -35394,10 +34546,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002305", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004135" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002306", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000239" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002306", "pred" : "is_a", @@ -35725,13 +34873,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000612", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002584", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0002584" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000612", "pred" : "is_a", @@ -35787,13 +34929,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000746", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_1000612", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_1000612" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000746", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35830,10 +34966,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_1000849", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001292" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_1000854", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0002584" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000854", "pred" : "is_a", @@ -35976,18 +35108,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_4033054", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002049" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000226", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007010" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000226", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0007017" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0000226", - "pred" : "http://purl.obolibrary.org/obo/RO_0002592", - "obj" : "http://purl.obolibrary.org/obo/GO_0015630" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000278", "pred" : "is_a", @@ -36024,18 +35144,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0001508", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0042391" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0001578", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0000226" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0001578", - "pred" : "http://purl.obolibrary.org/obo/RO_0000057", - "obj" : "http://purl.obolibrary.org/obo/GO_0005874" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0001578", - "pred" : "http://purl.obolibrary.org/obo/RO_0002297", - "obj" : "http://purl.obolibrary.org/obo/GO_0097427" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0001677", "pred" : "is_a", @@ -36370,34 +35478,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0005737", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0005622" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005773", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0043231" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005773", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0005737" - 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}, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0009058" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1901576", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0071704" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1903047", "pred" : "is_a", @@ -38510,18 +37094,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_1903561", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0065010" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1905349", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0022607" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1905349", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/GO_0060271" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_1905349", - "pred" : "http://purl.obolibrary.org/obo/RO_0002588", - "obj" : "http://purl.obolibrary.org/obo/GO_0035869" }, { "sub" : "http://purl.obolibrary.org/obo/GO_1990904", "pred" : "is_a", @@ -38786,6 +37358,10 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002045", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0000402" + }, { + "sub" : "http://purl.obolibrary.org/obo/PATO_0002064", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PATO_0000141" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002078", "pred" : "is_a", @@ -38802,10 +37378,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002198", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0001018" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002226", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0001873" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002266", "pred" : "is_a", @@ -38818,10 +37390,6 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0002299", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0002078" - }, { - "sub" : "http://purl.obolibrary.org/obo/PATO_0002309", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PATO_0002226" }, { "sub" : "http://purl.obolibrary.org/obo/PATO_0002318", "pred" : "is_a", @@ -38866,6 +37434,18 @@ "sub" : "http://purl.obolibrary.org/obo/PATO_0070047", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PATO_0070045" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000018263" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000000001", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0006412" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000001002", "pred" : "is_a", @@ -38998,6 +37578,10 @@ "sub" : "http://purl.obolibrary.org/obo/PR_000050025", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000025", "pred" : "is_a", @@ -46302,6 +44886,10 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" + }, { + "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", + "pred" : "inverseOf", + "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -46376,20 +44964,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0030219" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000064", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000067", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000068", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], @@ -46399,10 +44973,10 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000071", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000076" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0004638" + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", @@ -46679,6 +45253,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0002001" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000666", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000115" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002064" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000680", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0011115" ], @@ -47159,13 +45740,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002220", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000226", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0015630" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000278", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007049" ], @@ -47292,20 +45866,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007010", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005856" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007017", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007275", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], @@ -47379,13 +45939,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000479" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010970", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002341", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012501", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008219" ], @@ -47414,13 +45967,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0016192", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0017145", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051301" ], @@ -47533,27 +46079,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002315", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000556" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0030705", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0046907" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002341", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0099513" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031410", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0031503", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032060", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -47561,13 +46086,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032059" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032838", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0120025" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0032984", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022411" ], @@ -47575,13 +46093,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002590", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0033365", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0034101", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048872" ], @@ -47589,13 +46100,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0012003", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000232" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035082", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005930" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035148", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], @@ -47624,26 +46128,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0035735", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0042073" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0060271" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0042073", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002341", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0043073", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005634" ], @@ -47707,20 +46191,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002211", "fillerId" : "http://purl.obolibrary.org/obo/GO_0003008" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0044782", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0046907", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048103", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051301" ], @@ -47728,23 +46198,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", "fillerId" : "http://purl.obolibrary.org/obo/CL_0000723" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048193", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002344", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005798" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048199", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006903" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002344", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005794" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005798" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0048285", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], @@ -47829,41 +46282,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005694" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051640", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051648", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051179" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051649", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", - "fillerId" : "http://purl.obolibrary.org/obo/CL_0000000" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051650", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0031982" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0051656", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0051234" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0004009", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0055085", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], @@ -47871,13 +46289,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002342", "fillerId" : "http://purl.obolibrary.org/obo/GO_0016020" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060271", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0060429", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], @@ -47892,13 +46303,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002298", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003914" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0061512", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008104" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002339", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0065003", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -47955,20 +46359,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002297", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003914" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097014", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005929" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0097708", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0031982" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005622" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0098590", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -48014,33 +46404,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0015006" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099111", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006810" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002608", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005874" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099512", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0099080" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0002309" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0015006" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099513", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0099512" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005856" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", - "fillerId" : "http://purl.obolibrary.org/obo/PATO_0015006" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099536", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007267" ], @@ -48048,13 +46411,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000066", "fillerId" : "http://purl.obolibrary.org/obo/GO_0045202" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_0099568", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0005737" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0005737" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0120025", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0042995" ], @@ -48107,13 +46463,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005576" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/GO_1905349", - "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002588", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0035869" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/PR_000029032", "genusIds" : [ "http://purl.obolibrary.org/obo/PR_000000001" ], @@ -49186,14 +47535,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0005634", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005794", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0005929", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006915", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -49210,18 +47551,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0030097", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0042073", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0043009", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0044782", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045202", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -49230,22 +47563,6 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050877", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0051640", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0051649", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0060271", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0061512", - "pred" : "http://purl.obolibrary.org/obo/RO_0002162", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0062023", "pred" : "http://purl.obolibrary.org/obo/RO_0002162", @@ -49340,6 +47657,10 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0015016", "domainClassIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ] + }, { + "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002206", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] diff --git a/subsets/kidney_upper_slim.obo b/subsets/kidney_upper_slim.obo index 6bb9cf873..3f10ccd90 100644 --- a/subsets/kidney_upper_slim.obo +++ b/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-05-15/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-07-10/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,8 +89,13 @@ synonymtypedef: syngo_official_label "" synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" +idspace: dc http://purl.org/dc/elements/1.1/ +idspace: foaf http://xmlns.com/foaf/0.1/ +idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# +idspace: sssom https://w3id.org/sssom/ +idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-05-15" xsd:string +property_value: owl:versionInfo "2024-07-10" xsd:string [Term] id: CL:0000000 @@ -100,7 +105,7 @@ comment: The definition of cell is intended to represent all cells, and thus a c subset: cellxgene_subset subset: ubprop:upper_level xref: CALOHA:TS-2035 -xref: FBbt:00007002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:68646 xref: GO:0005623 xref: KUPO:0000002 @@ -108,7 +113,7 @@ xref: MESH:D002477 xref: VHOG:0001533 xref: WBbt:0004017 xref: XAO:0003012 -xref: ZFA:0009000 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex @@ -119,7 +124,7 @@ relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms id: CL:0000007 name: early embryonic cell (metazoa) def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm] -xref: ZFA:0009002 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) [Term] @@ -133,7 +138,7 @@ subset: human_reference_atlas synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 -xref: ZFA:0005957 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -158,7 +163,7 @@ xref: CALOHA:TS-0448 xref: FMA:86475 xref: MESH:D006412 xref: VHOG:0001485 -xref: ZFA:0009014 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009014 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell is_a: CL:0008001 ! hematopoietic precursor cell is_a: CL:0011026 ! progenitor cell @@ -206,7 +211,7 @@ synonym: "CFU-E" RELATED OMO:0003000 [] synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 -xref: ZFA:0009015 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell @@ -218,7 +223,7 @@ def: "A cell that is within the developmental lineage of gametes and is able to comment: Originally this term had some plant germ line cell children. subset: general_cell_types_upper_slim subset: ubprop:upper_level -xref: ZFA:0009016 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: capable_of GO:0022414 ! reproductive process @@ -231,7 +236,7 @@ synonym: "multifate stem cell" EXACT [] synonym: "multipotent cell" EXACT [] synonym: "multipotent stem cell" EXACT [] xref: FMA:84789 -xref: ZFA:0009020 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009020 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -254,7 +259,7 @@ synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437] synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 -xref: ZFA:0009021 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009021 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -273,7 +278,7 @@ synonym: "Meg/E progenitor" EXACT [] synonym: "megakaryocyte/erythrocyte progenitor" EXACT [] synonym: "megakaryocyte/erythroid progenitor cell" EXACT [] synonym: "MEP" EXACT [] -xref: ZFA:0009022 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009022 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell is_a: CL:0011026 ! progenitor cell @@ -291,7 +296,7 @@ def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm] synonym: "totipotential stem cell" EXACT [] xref: FMA:84790 xref: MESH:D039901 -xref: ZFA:0009024 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000723 ! somatic stem cell [Term] @@ -311,10 +316,10 @@ name: myoblast def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:D032446, PMID:21849021] xref: BTO:0000222 xref: CALOHA:TS-0650 -xref: FBbt:00005083 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005083 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:70335 xref: VHOG:0001529 -xref: ZFA:0009025 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009025 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000680 ! muscle precursor cell [Term] @@ -330,24 +335,11 @@ xref: CALOHA:TS-0362 xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 -xref: ZFA:0009026 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009026 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002320 ! connective tissue cell relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000064 -name: ciliated cell -def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm] -subset: cellxgene_subset -xref: VHOG:0001532 -xref: XAO:0000031 -xref: ZFA:0009032 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell -intersection_of: CL:0000000 ! cell -intersection_of: has_part GO:0005929 ! cilium -relationship: has_part GO:0005929 ! cilium - [Term] id: CL:0000066 name: epithelial cell @@ -359,33 +351,21 @@ synonym: "epitheliocyte" EXACT [] xref: BTO:0000414 xref: CALOHA:TS-2026 xref: CARO:0000077 -xref: FBbt:00000124 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:66768 xref: WBbt:0003672 -xref: ZFA:0009034 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000067 -name: ciliated epithelial cell -def: "An epithelial cell that has a cilia." [GOC:tfm] -subset: cellxgene_subset -xref: FMA:70605 -xref: ZFA:0009035 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000064 ! ciliated cell -is_a: CL:0000066 ! epithelial cell -intersection_of: CL:0000066 ! epithelial cell -intersection_of: has_part GO:0005929 ! cilium - [Term] id: CL:0000068 name: duct epithelial cell def: "An epithelial cell that is part of a duct." [https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset -xref: ZFA:0009372 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009372 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000058 ! duct @@ -397,12 +377,10 @@ name: blood vessel endothelial cell def: "An endothelial cell that lines the vasculature." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas -synonym: "cuboidal endothelial cell of vascular tree" EXACT [] -xref: ZFA:0009036 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell +xref: ZFA:0009036 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002139 ! endothelial cell of vascular tree -intersection_of: CL:0000076 ! squamous epithelial cell -intersection_of: part_of UBERON:0004638 ! blood vessel endothelium +intersection_of: CL:0000115 ! endothelial cell +intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 @@ -419,7 +397,7 @@ name: columnar/cuboidal epithelial cell def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." [GO:0002065, https://orcid.org/0000-0001-5208-3432] subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0009038 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009038 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -428,7 +406,7 @@ id: CL:0000076 name: squamous epithelial cell subset: cellxgene_subset xref: CALOHA:TS-1249 -xref: ZFA:0009039 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell [Term] @@ -439,7 +417,7 @@ subset: cellxgene_subset subset: general_cell_types_upper_slim xref: FMA:62844 xref: MESH:D001773 -xref: ZFA:0009044 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009044 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: capable_of GO:0008015 ! blood circulation @@ -456,9 +434,9 @@ synonym: "endotheliocyte" EXACT [] xref: BTO:0001176 xref: CALOHA:TS-0278 xref: FMA:66772 -xref: ZFA:0009065 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell -is_a: CL:0002078 ! meso-epithelial cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -466,7 +444,7 @@ id: CL:0000133 name: neurectodermal cell def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] synonym: "neurectoderm cell" EXACT [] -xref: ZFA:0009080 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009080 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000221 ! ectodermal cell [Term] @@ -490,7 +468,7 @@ synonym: "stem cells, mesenchymal" RELATED OMO:0003004 [MESH:D044982] xref: BTO:0002625 xref: BTO:0003298 xref: FMA:70546 -xref: ZFA:0009081 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009081 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/474" xsd:string @@ -533,14 +511,14 @@ synonym: "myocyte" EXACT [] xref: BTO:0000888 xref: BTO:0000902 xref: CALOHA:TS-2032 -xref: FBbt:00005074 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005074 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67328 xref: WBbt:0003675 -xref: ZFA:0009114 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -556,7 +534,7 @@ synonym: "smooth muscle fiber" EXACT [] xref: BTO:0004576 xref: CALOHA:TS-2159 xref: FMA:14072 -xref: ZFA:0009118 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009118 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast @@ -566,7 +544,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000211 name: electrically active cell def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] -xref: ZFA:0009128 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009128 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -574,21 +552,21 @@ id: CL:0000213 name: lining cell def: "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." [JB:jb] synonym: "boundary cell" EXACT [] -xref: ZFA:0009130 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009130 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000215 ! barrier cell [Term] id: CL:0000215 name: barrier cell def: "A cell whose primary function is to prevent the transport of stuff across compartments." [JB:jb] -xref: ZFA:0009132 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009132 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] id: CL:0000219 name: motile cell def: "A cell that moves by its own activities." [FB:ma] -xref: ZFA:0009136 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009136 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0048870 ! cell motility @@ -600,7 +578,7 @@ name: ectodermal cell def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475] synonym: "ectoderm cell" EXACT [] xref: FMA:72549 -xref: ZFA:0009137 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -612,7 +590,7 @@ subset: cellxgene_subset synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 -xref: ZFA:0009138 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -622,7 +600,7 @@ name: endodermal cell def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707] synonym: "endoderm cell" EXACT [] xref: FMA:72555 -xref: ZFA:0009139 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -653,13 +631,6 @@ relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin r relationship: RO:0002202 CL:0000558 ! develops from reticulocyte property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000239 -name: brush border epithelial cell -xref: ZFA:0009143 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000067 ! ciliated epithelial cell -is_a: CL:0000075 ! columnar/cuboidal epithelial cell - [Term] id: CL:0000255 name: eukaryotic cell @@ -675,7 +646,7 @@ relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota id: CL:0000329 name: oxygen accumulating cell def: "Any cell that is capable of some oxygen transport." [FBC:Autogenerated] -xref: ZFA:0009164 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009164 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0015671 ! oxygen transport @@ -686,7 +657,7 @@ id: CL:0000333 name: migratory neural crest cell def: "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." [doi:10.1016/j.stem.2015.02.017] xref: FMA:86667 -xref: ZFA:0007086 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007086 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell @@ -696,7 +667,7 @@ relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest ce id: CL:0000335 name: mesenchyme condensation cell def: "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." [GOC:tfm, PMID:5025404] -xref: ZFA:0009166 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009166 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008019 ! mesenchymal cell [Term] @@ -724,14 +695,14 @@ relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa id: CL:0000393 name: electrically responsive cell def: "A cell whose function is determined by its response to an electric signal." [FB:ma] -xref: ZFA:0009190 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009190 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] id: CL:0000404 name: electrically signaling cell def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] -xref: ZFA:0009193 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009193 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000211 ! electrically active cell [Term] @@ -742,7 +713,7 @@ subset: cellxgene_subset synonym: "myoblast, smooth muscle" EXACT [MESH:D032390] synonym: "satellite cell" RELATED [] xref: FMA:84798 -xref: ZFA:0009235 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009235 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell @@ -759,16 +730,16 @@ subset: human_reference_atlas synonym: "nerve cell" EXACT [] xref: BTO:0000938 xref: CALOHA:TS-0683 -xref: FBbt:00005106 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005106 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54527 xref: VHOG:0001483 xref: WBbt:0003679 -xref: ZFA:0009248 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009248 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -825,7 +796,7 @@ synonym: "early erythroblast" EXACT [ISBN:0721601464] synonym: "early normoblast" EXACT [ISBN:0721601464] synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 -xref: ZFA:0005236 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -846,7 +817,7 @@ synonym: "polychromatic normoblast" EXACT [ISBN:0721601464] synonym: "polychromatophilic normoblast" EXACT [ISBN:0721601464] synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 -xref: ZFA:0005241 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm @@ -959,7 +930,7 @@ subset: cellxgene_subset xref: BTO:0001173 xref: CALOHA:TS-0864 xref: MESH:D012156 -xref: ZFA:0009252 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly @@ -997,7 +968,7 @@ def: "A mesenchymal stem cell capable of developing into blood vessel endotheliu comment: These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. synonym: "angioblast" EXACT [] synonym: "chondroplast" EXACT [] -xref: ZFA:0009258 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell @@ -1028,7 +999,7 @@ def: "A cell whose primary function is to support other cell types." [FB:ma, GOC subset: cellxgene_subset synonym: "supportive cell" EXACT [] xref: BTO:0002315 -xref: ZFA:0009387 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009387 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1040,7 +1011,7 @@ synonym: "JG cell" EXACT [] synonym: "juxtaglomerular cell" BROAD [] synonym: "renin secreting cell" EXACT [] xref: FMA:84138 -xref: ZFA:0005238 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005238 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000192 ! smooth muscle cell is_a: CL:1000618 ! juxtaglomerular complex cell @@ -1061,17 +1032,21 @@ xref: BTO:0000853 xref: CALOHA:TS-0617 xref: FMA:70972 xref: MESH:D050527 -xref: ZFA:0009283 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009283 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000669 ! pericyte relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000666 -name: fenestrated cell +name: fenestrated endothelial cell +def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset synonym: "window cell" EXACT [] -xref: ZFA:0009286 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000066 ! epithelial cell +xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000115 ! endothelial cell +intersection_of: CL:0000115 ! endothelial cell +intersection_of: bearer_of PATO:0002064 ! fenestrated +relationship: bearer_of PATO:0002064 ! fenestrated [Term] id: CL:0000669 @@ -1088,7 +1063,7 @@ synonym: "pericyte cell" EXACT [] synonym: "pericyte of Rouget" EXACT [] xref: BTO:0002441 xref: FMA:63174 -xref: ZFA:0009112 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009112 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell @@ -1100,7 +1075,7 @@ id: CL:0000680 name: muscle precursor cell def: "A non-terminally differentiated cell that is capable of developing into a muscle cell." [GOC:add] subset: cellxgene_subset -xref: ZFA:0009291 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell @@ -1113,7 +1088,7 @@ name: somatic stem cell def: "A stem cell that can give rise to cell types of the body other than those of the germ-line." [GO:0048103] xref: CALOHA:TS-2086 xref: MESH:D053687 -xref: ZFA:0009307 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009307 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000034 ! stem cell intersection_of: CL:0000034 ! stem cell intersection_of: capable_of GO:0048103 ! somatic stem cell division @@ -1127,7 +1102,7 @@ subset: cellxgene_subset xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 -xref: ZFA:0009324 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1144,7 +1119,7 @@ synonym: "erythropoietic cell" EXACT [] xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 -xref: ZFA:0009325 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell property_value: RO:0002175 NCBITaxon:9606 @@ -1159,7 +1134,7 @@ xref: BTO:0001571 xref: CALOHA:TS-0289 xref: FMA:83504 xref: MESH:D004900 -xref: ZFA:0005237 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005237 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000764 ! erythroid lineage cell @@ -1205,7 +1180,7 @@ synonym: "hemopoietic progenitor cell" EXACT [] synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 -xref: ZFA:0009354 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent @@ -1253,7 +1228,7 @@ synonym: "myeloid progenitor cell" BROAD [] xref: BTO:0004730 xref: CALOHA:TS-2099 xref: FMA:70339 -xref: ZFA:0009356 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009356 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell @@ -1273,7 +1248,7 @@ xref: BTO:0000574 xref: CALOHA:TS-2017 xref: FMA:70366 xref: FMA:83598 -xref: ZFA:0005830 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005830 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell [Term] @@ -1287,7 +1262,7 @@ intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1301,7 +1276,7 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1309,12 +1284,12 @@ id: CL:0002077 name: ecto-epithelial cell def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 -xref: ZFA:0009385 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009385 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1323,12 +1298,12 @@ name: meso-epithelial cell def: "Epithelial cell derived from mesoderm or mesenchyme." [FMA:69076, GOC:tfm] synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 -xref: ZFA:0009388 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009388 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1343,7 +1318,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1361,7 +1336,7 @@ is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium relationship: part_of UBERON:0002321 ! extraglomerular mesangium -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:20:55Z [Term] @@ -1372,12 +1347,12 @@ subset: cellxgene_subset subset: kidney_upper_slim xref: BTO:0004632 xref: FMA:70970 -is_a: CL:0000115 {is_inferred="true"} ! endothelial cell -is_a: CL:0000666 ! fenestrated cell -is_a: CL:1000746 ! glomerular cell +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +relationship: part_of UBERON:0000074 ! renal glomerulus +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z [Term] @@ -1389,7 +1364,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1411,13 +1386,13 @@ relationship: part_of UBERON:0004135 ! distal tubule id: CL:0002306 name: epithelial cell of proximal tubule def: "An epithelial cell of the proximal tubule of the kidney." [GOC:tfm, ISBN:1-4160-2328-3] +comment: The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. subset: cellxgene_subset subset: human_reference_atlas subset: kidney_upper_slim synonym: "kidney proximal tubule epithelial cell" EXACT [] xref: FMA:70973 xref: KUPO:0001044 -is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000494 {is_inferred="true"} ! nephron tubule epithelial cell is_a: CL:1000615 ! kidney cortex tubule cell @@ -1437,7 +1412,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1448,12 +1423,12 @@ subset: cellxgene_subset xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 -xref: ZFA:0009392 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1463,9 +1438,9 @@ def: "A cell of the embryo." [FMA:0618947256] xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 -xref: ZFA:0007089 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007089 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1482,7 +1457,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1491,12 +1466,12 @@ name: kidney epithelial cell def: "An epithelial cell of the kidney." [GOC:tfm, KUPO:SJ] subset: cellxgene_subset xref: KUPO:0001019 -xref: ZFA:0009374 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009374 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 {is_inferred="true"} ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z [Term] @@ -1504,9 +1479,9 @@ id: CL:0002546 name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. -xref: ZFA:0005773 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000222 ! mesodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1527,7 +1502,7 @@ is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001225 ! cortex of kidney -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0956-8634 +property_value: terms:contributor https://orcid.org/0000-0002-0956-8634 creation_date: 2011-10-25T03:49:41Z [Term] @@ -1535,7 +1510,7 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset -xref: ZFA:0005322 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell @@ -1543,11 +1518,11 @@ is_a: CL:0002518 ! kidney epithelial cell id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] -xref: ZFA:0007084 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0007084 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0011012 ! neural crest cell relationship: part_of UBERON:0002342 ! neural crest relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -1567,7 +1542,7 @@ is_a: CL:0000988 ! hematopoietic cell id: CL:0008007 name: visceral muscle cell def: "A muscle cell that is part of some visceral muscle." [GOC:dos] -xref: FBbt:00005070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005070 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000187 ! muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:8600004 ! visceral muscle tissue @@ -1592,10 +1567,10 @@ def: "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas -xref: ZFA:0005944 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0005944 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:4033054 ! perivascular cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T17:33:55Z [Term] @@ -1623,7 +1598,7 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell relationship: RO:0002202 CL:0000034 ! develops from stem cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -1645,7 +1620,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -1656,7 +1631,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -1667,7 +1642,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -1734,7 +1709,7 @@ name: kidney cell def: "A cell that is part of a kidney." [] subset: cellxgene_subset xref: KUPO:0001010 -xref: ZFA:0009389 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002113 ! kidney @@ -1747,7 +1722,7 @@ def: "A cell that is part of kidney interstitium." [] subset: cellxgene_subset subset: kidney_upper_slim xref: KUPO:0001013 -xref: ZFA:0009390 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009390 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell is_a: CL:4030031 ! interstitial cell intersection_of: CL:1000497 ! kidney cell @@ -1759,7 +1734,7 @@ id: CL:1000504 name: kidney medulla cell def: "A cell that is part of a renal medulla." [PMID:22343825] xref: KUPO:0001017 -xref: ZFA:0009391 {mapping:justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +xref: ZFA:0009391 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0000362 ! renal medulla @@ -1827,7 +1802,7 @@ name: kidney corpuscule cell def: "Any renal cortical epithelial cell that is part of some renal corpuscle." [FBC:Autogenerated] subset: kidney_upper_slim xref: KUPO:0001021 -is_a: CL:0002584 {is_inferred="true"} ! renal cortical epithelial cell +is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000449 ! epithelial cell of nephron intersection_of: CL:0002584 ! renal cortical epithelial cell intersection_of: part_of UBERON:0001229 ! renal corpuscle @@ -1876,7 +1851,7 @@ id: CL:1000746 name: glomerular cell def: "Any kidney corpuscule cell that is part of some renal glomerulus." [FBC:Autogenerated] xref: KUPO:0001036 -is_a: CL:1000612 {is_inferred="true"} ! kidney corpuscule cell +is_a: CL:1000612 ! kidney corpuscule cell intersection_of: CL:1000612 ! kidney corpuscule cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus @@ -1915,7 +1890,6 @@ id: CL:1000854 name: kidney blood vessel cell def: "A blood vessel cell that is part of a kidney." [PMID:34843404] xref: KUPO:0001014 -is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel @@ -2025,7 +1999,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue -property_value: http://purl.org/dc/terms/date "2022-11-30T14:35:08Z" xsd:dateTime +property_value: terms:date "2022-11-30T14:35:08Z" xsd:dateTime [Term] id: CL:4033054 @@ -2035,31 +2009,15 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature relationship: adjacent_to UBERON:0002049 ! vasculature -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-08-22T13:40:28Z" xsd:dateTime - -[Term] -id: GO:0000226 -name: microtubule cytoskeleton organization -namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] -subset: goslim_pombe -synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah] -synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah] -is_a: GO:0007010 ! cytoskeleton organization -is_a: GO:0007017 ! microtubule-based process -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0015630 ! microtubule cytoskeleton -relationship: results_in_organization_of GO:0015630 ! microtubule cytoskeleton -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23114" xsd:anyURI -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23195" xsd:anyURI +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process alt_id: GO:0007067 -def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] +def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194] comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle. subset: goslim_chembl subset: goslim_drosophila @@ -2126,16 +2084,6 @@ comment: Action potentials typically propagate across excitable membranes. This is_a: GO:0042391 ! regulation of membrane potential property_value: RO:0002161 NCBITaxon:4895 -[Term] -id: GO:0001578 -name: microtubule bundle formation -namespace: biological_process -def: "A process that results in a parallel arrangement of microtubules." [GOC:dph] -synonym: "microtubule bundling" EXACT [] -is_a: GO:0000226 ! microtubule cytoskeleton organization -relationship: has_participant GO:0005874 ! microtubule -relationship: results_in_formation_of GO:0097427 ! microtubule bundle - [Term] id: GO:0001677 name: formation of translation initiation ternary complex @@ -2657,67 +2605,6 @@ is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005622 ! intracellular anatomical structure property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23023" xsd:anyURI -[Term] -id: GO:0005773 -name: vacuole -namespace: cellular_component -def: "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." [GOC:mtg_sensu, ISBN:0198506732] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_yeast -synonym: "vacuolar carboxypeptidase Y" RELATED [] -xref: Wikipedia:Vacuole -is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: part_of GO:0005737 ! cytoplasm - -[Term] -id: GO:0005794 -name: Golgi apparatus -namespace: cellular_component -def: "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways." [ISBN:0198506732] -comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_generic -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_yeast -synonym: "Golgi" BROAD [] -synonym: "Golgi complex" EXACT [] -synonym: "Golgi ribbon" NARROW [] -xref: NIF_Subcellular:sao451912436 -xref: Wikipedia:Golgi_apparatus -is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0012505 ! endomembrane system -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota - -[Term] -id: GO:0005798 -name: Golgi-associated vesicle -namespace: cellular_component -def: "Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell." [GOC:mah] -comment: Note that this definition includes vesicles that are transiently associated with the Golgi. -synonym: "Golgi vesicle" RELATED [] -synonym: "vesicular component" RELATED [NIF_Subcellular:sao138219748] -xref: NIF_Subcellular:sao819927218 -is_a: GO:0031410 ! cytoplasmic vesicle - [Term] id: GO:0005840 name: ribosome @@ -2744,41 +2631,6 @@ is_a: GO:0043232 ! intracellular non-membrane-bounded organelle relationship: capable_of_part_of GO:0006412 ! translation relationship: has_part PR:000000001 ! protein -[Term] -id: GO:0005856 -name: cytoskeleton -namespace: cellular_component -def: "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." [GOC:mah, PMID:16959967, PMID:27419875] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_flybase_ribbon -subset: goslim_generic -subset: goslim_mouse -subset: goslim_pir -subset: goslim_plant -subset: goslim_plant_ribbon -subset: goslim_prokaryote -subset: goslim_yeast -xref: Wikipedia:Cytoskeleton -is_a: GO:0043232 ! intracellular non-membrane-bounded organelle - -[Term] -id: GO:0005874 -name: microtubule -namespace: cellular_component -def: "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." [ISBN:0879693568] -subset: goslim_metagenomics -synonym: "microtubuli" EXACT [] -synonym: "microtubulus" EXACT [] -synonym: "neurotubule" NARROW [NIF_Subcellular:sao248349196] -xref: NIF_Subcellular:sao1846835077 -xref: Wikipedia:Microtubule -is_a: GO:0099513 ! polymeric cytoskeletal fiber -relationship: part_of GO:0015630 ! microtubule cytoskeleton - [Term] id: GO:0005886 name: plasma membrane @@ -2826,55 +2678,6 @@ xref: NIF_Subcellular:sao1922892319 is_a: GO:0070161 ! anchoring junction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22122" xsd:anyURI -[Term] -id: GO:0005929 -name: cilium -namespace: cellular_component -alt_id: GO:0072372 -def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." [GOC:cilia, GOC:curators, GOC:kmv, GOC:vw, ISBN:0198547684, PMID:16824949, PMID:17009929, PMID:20144998] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_pir -synonym: "eukaryotic flagellum" EXACT [] -synonym: "flagellum" RELATED [] -synonym: "microtubule-based flagellum" EXACT [] -synonym: "primary cilium" NARROW [] -xref: FMA:67181 -xref: NIF_Subcellular:sao787716553 -xref: Wikipedia:Cilium -is_a: GO:0043227 ! membrane-bounded organelle -is_a: GO:0120025 ! plasma membrane bounded cell projection -relationship: has_part GO:0030990 ! intraciliary transport particle -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 - -[Term] -id: GO:0005930 -name: axoneme -namespace: cellular_component -alt_id: GO:0035085 -alt_id: GO:0035086 -def: "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, ISBN:0198547684] -comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. -subset: goslim_pir -synonym: "ciliary axoneme" EXACT [] -synonym: "cilium axoneme" EXACT [] -synonym: "flagellar axoneme" EXACT [] -synonym: "flagellum axoneme" EXACT [] -xref: Wikipedia:Axoneme -is_a: GO:0110165 ! cellular anatomical entity -relationship: has_part GO:0005874 ! microtubule -relationship: part_of GO:0005856 ! cytoskeleton -relationship: part_of GO:0097014 ! ciliary plasm - [Term] id: GO:0006412 name: translation @@ -2990,15 +2793,6 @@ namespace: biological_process def: "The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] is_a: GO:0042044 ! fluid transport -[Term] -id: GO:0006903 -name: vesicle targeting -namespace: biological_process -def: "The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo." [GOC:mah, PMID:17335816] -is_a: GO:0009987 ! cellular process -relationship: part_of GO:0016192 ! vesicle-mediated transport -relationship: part_of GO:0051650 ! establishment of vesicle localization - [Term] id: GO:0006915 name: apoptotic process @@ -3076,47 +2870,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-19T15:25:51Z -[Term] -id: GO:0007010 -name: cytoskeleton organization -namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." [GOC:dph, GOC:jl, GOC:mah] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_generic -subset: goslim_prokaryote -subset: goslim_yeast -synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah] -synonym: "cytoskeletal regulator activity" RELATED [] -synonym: "cytoskeleton organisation" EXACT [] -synonym: "cytoskeleton organization and biogenesis" RELATED [GOC:mah] -is_a: GO:0006996 ! organelle organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0005856 ! cytoskeleton -relationship: results_in_organization_of GO:0005856 ! cytoskeleton - -[Term] -id: GO:0007017 -name: microtubule-based process -namespace: biological_process -def: "Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins." [GOC:mah] -subset: goslim_chembl -is_a: GO:0009987 ! cellular process -intersection_of: GO:0009987 ! cellular process -intersection_of: process_has_causal_agent GO:0005874 ! microtubule -relationship: process_has_causal_agent GO:0005874 ! microtubule -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI - -[Term] -id: GO:0007018 -name: microtubule-based movement -namespace: biological_process -def: "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194] -subset: goslim_drosophila -subset: goslim_generic -is_a: GO:0007017 ! microtubule-based process - [Term] id: GO:0007049 name: cell cycle @@ -3454,7 +3207,6 @@ synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044249 ! cellular biosynthetic process -is_a: GO:1901576 ! organic substance biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15249" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25418" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI @@ -3591,23 +3343,6 @@ is_a: GO:0009059 ! macromolecule biosynthetic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22557" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25419" xsd:anyURI -[Term] -id: GO:0010970 -name: transport along microtubule -namespace: biological_process -def: "The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity." [GOC:dph, GOC:mah, GOC:tb] -synonym: "establishment of localization by movement along microtubule" EXACT [GOC:dph] -synonym: "microtubule-based transport" BROAD [] -synonym: "movement along microtubule" EXACT [] -is_a: GO:0007018 ! microtubule-based movement -is_a: GO:0030705 ! cytoskeleton-dependent intracellular transport -is_a: GO:0099111 ! microtubule-based transport -intersection_of: GO:0006810 ! transport -intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: results_in_transport_along GO:0005874 ! microtubule -created_by: tb -creation_date: 2009-05-27T10:56:08Z - [Term] id: GO:0012501 name: programmed cell death @@ -3638,20 +3373,6 @@ intersection_of: starts_with GO:0007165 ! signal transduction relationship: starts_with GO:0007165 ! signal transduction property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24835" xsd:anyURI -[Term] -id: GO:0012505 -name: endomembrane system -namespace: cellular_component -def: "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." [GOC:lh] -subset: goslim_candida -subset: goslim_flybase_ribbon -subset: goslim_yeast -xref: Wikipedia:Endomembrane_system -is_a: GO:0110165 ! cellular anatomical entity -relationship: has_part GO:0005773 ! vacuole -relationship: has_part GO:0005886 ! plasma membrane -relationship: part_of CL:0000000 ! cell - [Term] id: GO:0015031 name: protein transport @@ -3662,18 +3383,11 @@ subset: goslim_chembl subset: goslim_pir subset: goslim_yeast synonym: "enzyme transport" NARROW [] +is_a: GO:0006810 ! transport is_a: GO:0045184 ! establishment of protein localization -is_a: GO:0071702 ! organic substance transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input PR:000000001 ! protein -[Term] -id: GO:0015630 -name: microtubule cytoskeleton -namespace: cellular_component -def: "The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins." [GOC:jl, ISBN:0395825172] -is_a: GO:0005856 ! cytoskeleton - [Term] id: GO:0015669 name: gas transport @@ -3754,31 +3468,6 @@ intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0031982 ! vesicle relationship: results_in_organization_of GO:0031982 ! vesicle -[Term] -id: GO:0016192 -name: vesicle-mediated transport -namespace: biological_process -alt_id: GO:0006899 -def: "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." [GOC:ai, GOC:mah, ISBN:08789310662000] -subset: goslim_candida -subset: goslim_chembl -subset: goslim_drosophila -subset: goslim_euk_cellular_processes_ribbon -subset: goslim_generic -subset: goslim_pir -subset: goslim_pombe -synonym: "nonselective vesicle transport" NARROW [] -synonym: "protein sorting along secretory pathway" RELATED [] -synonym: "vesicle trafficking" RELATED [] -synonym: "vesicle transport" EXACT [] -synonym: "vesicular transport" EXACT [GOC:mah] -is_a: GO:0006810 ! transport -is_a: GO:0009987 ! cellular process -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0031982 ! vesicle -relationship: process_has_causal_agent GO:0031982 ! vesicle -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25421" xsd:anyURI - [Term] id: GO:0016331 name: morphogenesis of embryonic epithelium @@ -3885,14 +3574,6 @@ intersection_of: GO:0009987 ! cellular process intersection_of: part_of GO:0007049 ! cell cycle relationship: part_of GO:0007049 ! cell cycle -[Term] -id: GO:0022406 -name: membrane docking -namespace: biological_process -def: "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere." [GOC:isa_complete, PMID:27875684] -subset: goslim_pir -is_a: GO:0009987 ! cellular process - [Term] id: GO:0022411 name: cellular component disassembly @@ -4027,7 +3708,7 @@ creation_date: 2010-02-16T09:30:50Z id: GO:0030030 name: cell projection organization namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:16318917] subset: goslim_prokaryote synonym: "cell projection organisation" EXACT [] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] @@ -4042,7 +3723,7 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i id: GO:0030031 name: cell projection assembly namespace: biological_process -def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] +def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, PMID:18391171] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly @@ -4055,7 +3736,7 @@ relationship: results_in_assembly_of GO:0042995 ! cell projection id: GO:0030054 name: cell junction namespace: cellular_component -def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html, ISBN:0198506732, PMID:26820516, PMID:28096264] +def: "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." [GOC:aruk, GOC:bc, GOC:mah, ISBN:0198506732, PMID:26820516, PMID:28096264] subset: goslim_agr subset: goslim_drosophila subset: goslim_flybase_ribbon @@ -4182,31 +3863,6 @@ is_a: GO:0110165 ! cellular anatomical entity relationship: part_of CL:0000000 ! cell relationship: part_of GO:0071944 ! cell periphery -[Term] -id: GO:0030705 -name: cytoskeleton-dependent intracellular transport -namespace: biological_process -def: "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell." [GOC:mah] -subset: goslim_chembl -subset: goslim_drosophila -is_a: GO:0046907 ! intracellular transport -intersection_of: GO:0046907 ! intracellular transport -intersection_of: results_in_transport_along GO:0099513 ! polymeric cytoskeletal fiber -relationship: results_in_transport_along GO:0099513 ! polymeric cytoskeletal fiber - -[Term] -id: GO:0030990 -name: intraciliary transport particle -namespace: cellular_component -def: "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules." [GOC:cilia, GOC:kmv, PMID:14570576, PMID:22118932, PMID:23945166] -comment: Note that we deem cilia and microtubule-based flagella to be equivalent. -subset: goslim_pir -synonym: "IFT complex" RELATED [] -synonym: "intraflagellar transport complex" EXACT [] -synonym: "intraflagellar transport particle" EXACT [] -is_a: GO:0032991 ! protein-containing complex -relationship: capable_of_part_of GO:0035735 ! intraciliary transport involved in cilium assembly - [Term] id: GO:0031012 name: extracellular matrix @@ -4227,46 +3883,6 @@ is_a: GO:0030312 ! external encapsulating structure disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -[Term] -id: GO:0031410 -name: cytoplasmic vesicle -namespace: cellular_component -alt_id: GO:0016023 -def: "A vesicle found in the cytoplasm of a cell." [GOC:ai, GOC:mah, GOC:vesicles] -subset: goslim_agr -subset: goslim_candida -subset: goslim_chembl -subset: goslim_generic -subset: goslim_mouse -subset: goslim_yeast -synonym: "cytoplasmic membrane bounded vesicle" RELATED [] -synonym: "cytoplasmic membrane-enclosed vesicle" RELATED [] -synonym: "cytoplasmic, membrane-bounded vesicle" RELATED [] -xref: NIF_Subcellular:sao180601769 -is_a: GO:0097708 ! intracellular vesicle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - -[Term] -id: GO:0031503 -name: protein-containing complex localization -namespace: biological_process -alt_id: GO:0034629 -def: "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location." [GOC:mah] -synonym: "cellular protein complex localisation" RELATED [GOC:mah] -synonym: "cellular protein complex localization" RELATED [] -synonym: "cellular protein-containing complex localization" RELATED [] -synonym: "establishment and maintenance of cellular protein complex localization" RELATED [] -synonym: "establishment and maintenance of protein complex localization" EXACT [] -synonym: "protein complex localisation" EXACT [GOC:mah] -synonym: "protein complex localization" RELATED [] -is_a: GO:0051179 ! localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0032991 ! protein-containing complex -relationship: has_primary_input GO:0032991 ! protein-containing complex -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22021" xsd:anyURI - [Term] id: GO:0031974 name: membrane-enclosed lumen @@ -4357,16 +3973,6 @@ is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-19T12:21:31Z -[Term] -id: GO:0032838 -name: plasma membrane bounded cell projection cytoplasm -namespace: cellular_component -def: "All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection." [GOC:krc, GOC:mah] -is_a: GO:0099568 ! cytoplasmic region -intersection_of: GO:0005737 ! cytoplasm -intersection_of: part_of GO:0120025 ! plasma membrane bounded cell projection -relationship: part_of GO:0120025 ! plasma membrane bounded cell projection - [Term] id: GO:0032940 name: secretion by cell @@ -4437,18 +4043,6 @@ subset: goslim_flybase_ribbon synonym: "macromolecule localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization -[Term] -id: GO:0033365 -name: protein localization to organelle -namespace: biological_process -def: "A process in which a protein is transported to, or maintained in, a location within an organelle." [GOC:mah] -synonym: "protein localisation to organelle" EXACT [GOC:mah] -synonym: "protein localization in organelle" EXACT [GOC:mah] -is_a: GO:0008104 ! protein localization -intersection_of: GO:0008104 ! protein localization -intersection_of: has_target_end_location GO:0043226 ! organelle -relationship: has_target_end_location GO:0043226 ! organelle - [Term] id: GO:0034101 name: erythrocyte homeostasis @@ -4475,27 +4069,6 @@ synonym: "transmembrane ion transport" EXACT [GOC:dph, GOC:tb] is_a: GO:0006811 ! monoatomic ion transport is_a: GO:0055085 ! transmembrane transport -[Term] -id: GO:0035082 -name: axoneme assembly -namespace: biological_process -alt_id: GO:0035083 -alt_id: GO:0035084 -def: "The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." [GOC:bf, GOC:cilia, GOC:jl, ISBN:0815316194] -comment: Note that cilia and eukaryotic flagella are deemed to be equivalent. -synonym: "axoneme biogenesis" RELATED [GOC:mah] -synonym: "ciliary axoneme assembly" EXACT [] -synonym: "cilium axoneme assembly" EXACT [] -synonym: "cilium axoneme biogenesis" RELATED [GOC:mah] -synonym: "flagellar axoneme assembly" EXACT [] -synonym: "flagellum axoneme assembly" EXACT [] -is_a: GO:0001578 ! microtubule bundle formation -is_a: GO:0022607 ! cellular component assembly -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0005930 ! axoneme -relationship: part_of GO:0060271 ! cilium assembly -relationship: results_in_assembly_of GO:0005930 ! axoneme - [Term] id: GO:0035148 name: tube formation @@ -4545,36 +4118,6 @@ intersection_of: has_target_end_location GO:0005576 ! extracellular region created_by: bf creation_date: 2010-11-09T10:25:08Z -[Term] -id: GO:0035735 -name: intraciliary transport involved in cilium assembly -namespace: biological_process -def: "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly." [GOC:bf, GOC:cilia, Reactome:R-HSA-5620924.2] -synonym: "intraciliary transport involved in cilium morphogenesis" RELATED [] -synonym: "intraflagellar transport" BROAD [] -synonym: "intraflagellar transport involved in cilium morphogenesis" RELATED [] -xref: Reactome:R-HSA-5620924.2 -is_a: GO:0042073 ! intraciliary transport -intersection_of: GO:0042073 ! intraciliary transport -intersection_of: part_of GO:0060271 ! cilium assembly -relationship: part_of GO:0060271 ! cilium assembly -created_by: bf -creation_date: 2011-03-17T10:55:42Z - -[Term] -id: GO:0035869 -name: ciliary transition zone -namespace: cellular_component -def: "A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm." [GOC:cilia, GOC:kmv, PMID:21422230] -comment: Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone. -synonym: "cilial transition zone" EXACT [] -synonym: "cilium transition zone" EXACT [] -synonym: "connecting cilium" RELATED [] -is_a: GO:0110165 ! cellular anatomical entity -relationship: part_of GO:0005929 ! cilium -created_by: bf -creation_date: 2011-05-25T03:09:58Z - [Term] id: GO:0040011 name: locomotion @@ -4601,35 +4144,6 @@ def: "The directed movement of substances that are in liquid form in normal livi subset: goslim_pir is_a: GO:0006810 ! transport -[Term] -id: GO:0042073 -name: intraciliary transport -namespace: biological_process -alt_id: GO:0035734 -def: "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." [GOC:cilia, GOC:kmv, PMID:17981739, PMID:18180368, PMID:22869374, Reactome:R-HSA-5620924.2] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. -synonym: "IFT" RELATED [] -synonym: "intraflagellar transport" EXACT [] -synonym: "intraflagellar transport involved in cilium organization" EXACT [] -synonym: "intraflagellar transport involved in microtubule-based flagellum organisation" EXACT [] -xref: Wikipedia:Intraflagellar_transport -is_a: GO:0010970 ! transport along microtubule -is_a: GO:0031503 ! protein-containing complex localization -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input GO:0032991 ! protein-containing complex -intersection_of: occurs_in GO:0005929 ! cilium -intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: occurs_in GO:0005929 ! cilium -relationship: part_of GO:0044782 ! cilium organization -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 - [Term] id: GO:0042391 name: regulation of membrane potential @@ -4660,7 +4174,7 @@ is_a: GO:0008150 ! biological_process id: GO:0042995 name: cell projection namespace: cellular_component -def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] +def: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, PMID:16318917] subset: goslim_agr subset: goslim_euk_cellular_processes_ribbon subset: goslim_flybase_ribbon @@ -4881,13 +4395,14 @@ is_a: GO:0009987 ! cellular process id: GO:0044238 name: primary metabolic process namespace: biological_process -def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] +def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_euk_cellular_processes_ribbon subset: goslim_pir subset: goslim_plant_ribbon subset: goslim_prokaryote_ribbon synonym: "primary metabolism" EXACT [] +xref: Wikipedia:Primary_metabolite is_a: GO:0008152 ! metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -4906,25 +4421,6 @@ is_a: GO:0009058 ! biosynthetic process is_a: GO:0044237 ! cellular metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27052" xsd:anyURI -[Term] -id: GO:0044782 -name: cilium organization -namespace: biological_process -def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:cilia, GOC:jl] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. -subset: goslim_drosophila -subset: goslim_generic -synonym: "microtubule-based flagellum organization" EXACT [] -is_a: GO:0006996 ! organelle organization -is_a: GO:0120036 ! plasma membrane bounded cell projection organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0005929 ! cilium -relationship: results_in_organization_of GO:0005929 ! cilium -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -created_by: jl -creation_date: 2013-03-27T15:09:58Z - [Term] id: GO:0045184 name: establishment of protein localization @@ -4965,23 +4461,6 @@ def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport -[Term] -id: GO:0046907 -name: intracellular transport -namespace: biological_process -alt_id: GO:1902582 -def: "The directed movement of substances within a cell." [GOC:ai] -synonym: "single organism intracellular transport" RELATED [GOC:TermGenie] -synonym: "single-organism intracellular transport" RELATED [] -is_a: GO:0006810 ! transport -is_a: GO:0051641 ! cellular localization -is_a: GO:0051649 ! establishment of localization in cell -intersection_of: GO:0006810 ! transport -intersection_of: occurs_in GO:0005622 ! intracellular anatomical structure -relationship: occurs_in GO:0005622 ! intracellular anatomical structure -created_by: jl -creation_date: 2013-12-18T14:04:50Z - [Term] id: GO:0048103 name: somatic stem cell division @@ -4993,34 +4472,6 @@ intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000723 ! somatic stem cell relationship: has_primary_input CL:0000723 ! somatic stem cell -[Term] -id: GO:0048193 -name: Golgi vesicle transport -namespace: biological_process -def: "The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles." [GOC:jid, ISBN:0716731363, PMID:10219233] -subset: goslim_yeast -synonym: "Golgi-derived vesicle transport" RELATED [] -is_a: GO:0016192 ! vesicle-mediated transport -intersection_of: GO:0006810 ! transport -intersection_of: results_in_transport_to_from_or_in GO:0005798 ! Golgi-associated vesicle -relationship: results_in_transport_to_from_or_in GO:0005798 ! Golgi-associated vesicle - -[Term] -id: GO:0048199 -name: vesicle targeting, to, from or within Golgi -namespace: biological_process -def: "The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation." [GOC:jid, GOC:mah, ISBN:0716731363, PMID:10219233] -synonym: "dictyosome vesicle targeting" NARROW [] -synonym: "Golgi vesicle targeting" EXACT [] -synonym: "vesicle targeting, to, from or within dictyosome" NARROW [] -is_a: GO:0006903 ! vesicle targeting -intersection_of: GO:0006903 ! vesicle targeting -intersection_of: has_primary_input GO:0005798 ! Golgi-associated vesicle -intersection_of: results_in_transport_to_from_or_in GO:0005794 ! Golgi apparatus -relationship: has_primary_input GO:0005798 ! Golgi-associated vesicle -relationship: part_of GO:0048193 ! Golgi vesicle transport -relationship: results_in_transport_to_from_or_in GO:0005794 ! Golgi apparatus - [Term] id: GO:0048285 name: organelle fission @@ -5374,22 +4825,6 @@ subset: goslim_pir xref: Wikipedia:Cell_division is_a: GO:0009987 ! cellular process -[Term] -id: GO:0051640 -name: organelle localization -namespace: biological_process -def: "Any process in which an organelle is transported to, and/or maintained in, a specific location." [GOC:ai] -subset: goslim_pir -synonym: "establishment and maintenance of organelle localization" EXACT [] -synonym: "organelle localisation" EXACT [GOC:mah] -is_a: GO:0051179 ! localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0043226 ! organelle -relationship: has_primary_input GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI - [Term] id: GO:0051641 name: cellular localization @@ -5412,60 +4847,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-18T14:04:32Z -[Term] -id: GO:0051648 -name: vesicle localization -namespace: biological_process -def: "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." [GOC:ai] -synonym: "cytoplasmic vesicle localization" EXACT [] -synonym: "establishment and maintenance of vesicle localization" EXACT [] -synonym: "vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051640 ! organelle localization -intersection_of: GO:0051179 ! localization -intersection_of: has_primary_input GO:0031982 ! vesicle -relationship: has_primary_input GO:0031982 ! vesicle - -[Term] -id: GO:0051649 -name: establishment of localization in cell -namespace: biological_process -def: "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos, GOC:dph, GOC:tb] -synonym: "establishment of cellular localization" RELATED [GOC:dph, GOC:tb] -synonym: "establishment of intracellular localization" NARROW [] -synonym: "establishment of localisation in cell" EXACT [GOC:mah] -synonym: "establishment of localization within cell" NARROW [] -synonym: "positioning within cell" NARROW [] -is_a: GO:0051234 ! establishment of localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: occurs_in CL:0000000 ! cell -relationship: occurs_in CL:0000000 ! cell -relationship: part_of GO:0051641 ! cellular localization -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms -relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms - -[Term] -id: GO:0051650 -name: establishment of vesicle localization -namespace: biological_process -def: "The directed movement of a vesicle to a specific location." [GOC:ai] -synonym: "establishment of vesicle localisation" EXACT [GOC:mah] -is_a: GO:0051648 ! vesicle localization -is_a: GO:0051649 ! establishment of localization in cell -is_a: GO:0051656 ! establishment of organelle localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: has_primary_input GO:0031982 ! vesicle - -[Term] -id: GO:0051656 -name: establishment of organelle localization -namespace: biological_process -def: "The directed movement of an organelle to a specific location." [GOC:ai] -synonym: "establishment of organelle localisation" EXACT [GOC:mah] -is_a: GO:0051234 ! establishment of localization -is_a: GO:0051640 ! organelle localization -intersection_of: GO:0051234 ! establishment of localization -intersection_of: has_primary_input GO:0043226 ! organelle - [Term] id: GO:0051716 name: cellular response to stimulus @@ -5510,40 +4891,6 @@ xref: Wikipedia:Urination is_a: GO:0003014 ! renal system process is_a: GO:0007588 ! excretion -[Term] -id: GO:0060271 -name: cilium assembly -namespace: biological_process -alt_id: GO:0042384 -def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. -synonym: "ciliogenesis" EXACT [] -synonym: "cilium biogenesis" RELATED [GOC:mah] -synonym: "cilium formation" EXACT [] -synonym: "cilium morphogenesis" RELATED [] -synonym: "cilium organization" RELATED [GOC:dph] -synonym: "microtubule-based flagellum assembly" EXACT [] -xref: Reactome:R-HSA-5617833.2 -is_a: GO:0044782 ! cilium organization -is_a: GO:0070925 ! organelle assembly -is_a: GO:0120031 ! plasma membrane bounded cell projection assembly -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0005929 ! cilium -relationship: has_part GO:0035082 ! axoneme assembly -relationship: has_part GO:0035735 ! intraciliary transport involved in cilium assembly -relationship: has_part GO:0061512 ! protein localization to cilium -relationship: has_part GO:0097712 ! vesicle targeting, trans-Golgi to periciliary membrane compartment -relationship: has_part GO:1905349 ! ciliary transition zone assembly -relationship: results_in_assembly_of GO:0005929 ! cilium -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -relationship: starts_with GO:0097711 ! ciliary basal body-plasma membrane docking -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 - [Term] id: GO:0060429 name: epithelium development @@ -5578,26 +4925,6 @@ is_a: GO:0002009 ! morphogenesis of an epithelium created_by: dph creation_date: 2010-05-25T09:05:34Z -[Term] -id: GO:0061512 -name: protein localization to cilium -namespace: biological_process -def: "A process in which a protein is transported to, or maintained in, a location within a cilium." [GOC:dph] -is_a: GO:0033365 ! protein localization to organelle -intersection_of: GO:0008104 ! protein localization -intersection_of: has_target_end_location GO:0005929 ! cilium -relationship: has_target_end_location GO:0005929 ! cilium -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota -property_value: RO:0002161 NCBITaxon:3176 -property_value: RO:0002161 NCBITaxon:3312 -property_value: RO:0002161 NCBITaxon:3378 -property_value: RO:0002161 NCBITaxon:3398 -property_value: RO:0002161 NCBITaxon:4890 -property_value: RO:0002161 NCBITaxon:5782 -created_by: dph -creation_date: 2013-03-22T15:41:44Z - [Term] id: GO:0062023 name: collagen-containing extracellular matrix @@ -5756,29 +5083,6 @@ relationship: has_target_end_location GO:0005576 ! extracellular region created_by: mah creation_date: 2010-02-25T04:00:13Z -[Term] -id: GO:0071702 -name: organic substance transport -namespace: biological_process -def: "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [GOC:mah] -is_a: GO:0006810 ! transport -created_by: mah -creation_date: 2010-03-08T02:15:14Z - -[Term] -id: GO:0071704 -name: organic substance metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [GOC:mah] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity metabolic process" EXACT [] -synonym: "organic molecular entity metabolism" EXACT [] -synonym: "organic substance metabolism" EXACT [] -is_a: GO:0008152 ! metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: mah -creation_date: 2010-03-08T03:32:18Z - [Term] id: GO:0071826 name: protein-RNA complex organization @@ -5853,27 +5157,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: mah creation_date: 2010-02-26T02:15:40Z -[Term] -id: GO:0097014 -name: ciliary plasm -namespace: cellular_component -def: "All of the contents of a cilium, excluding the plasma membrane surrounding the cilium." [GOC:BHF, GOC:cilia, GOC:dos, PMID:17895364] -comment: Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". -synonym: "cilial cytoplasm" RELATED [] -synonym: "ciliary cytoplasm" RELATED [] -synonym: "cilium cytoplasm" RELATED [] -synonym: "cilium plasm" EXACT [] -synonym: "microtubule-based flagellar cytoplasm" RELATED [] -synonym: "microtubule-based flagellar matrix" NARROW [] -synonym: "microtubule-based flagellum cytoplasm" RELATED [] -synonym: "microtubule-based flagellum matrix" NARROW [] -is_a: GO:0032838 ! plasma membrane bounded cell projection cytoplasm -intersection_of: GO:0005737 ! cytoplasm -intersection_of: part_of GO:0005929 ! cilium -relationship: part_of GO:0005929 ! cilium -created_by: pr -creation_date: 2011-03-23T01:52:31Z - [Term] id: GO:0097190 name: apoptotic signaling pathway @@ -5921,55 +5204,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pr creation_date: 2012-03-05T02:03:58Z -[Term] -id: GO:0097427 -name: microtubule bundle -namespace: cellular_component -def: "An arrangement of closely apposed microtubules running parallel to each other." [NIF_Subcellular:sao1872343973] -synonym: "microtubule fascicle" EXACT [] -xref: NIF_Subcellular:sao1872343973 -is_a: GO:0110165 ! cellular anatomical entity -relationship: has_part GO:0005874 ! microtubule -relationship: part_of GO:0005856 ! cytoskeleton -created_by: pr -creation_date: 2012-11-07T15:01:27Z - -[Term] -id: GO:0097708 -name: intracellular vesicle -namespace: cellular_component -def: "Any vesicle that is part of the intracellular region." [GOC:vesicles] -is_a: GO:0031982 ! vesicle -is_a: GO:0043231 ! intracellular membrane-bounded organelle -intersection_of: GO:0031982 ! vesicle -intersection_of: part_of GO:0005622 ! intracellular anatomical structure -created_by: pr -creation_date: 2016-03-29T17:39:45Z - -[Term] -id: GO:0097711 -name: ciliary basal body-plasma membrane docking -namespace: biological_process -def: "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane." [GOC:cilia, PMID:13978319, PMID:23348840, PMID:23530209, PMID:25686250, PMID:26981235, Reactome:R-HSA-5620912.1] -comment: Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella. -synonym: "anchoring of the basal body to the plasma membrane" RELATED [] -synonym: "ciliary basal body docking" EXACT [] -xref: Reactome:R-HSA-5620912.1 -is_a: GO:0140056 ! organelle localization by membrane tethering -relationship: part_of GO:0060271 ! cilium assembly -created_by: pr -creation_date: 2016-08-05T16:12:33Z - -[Term] -id: GO:0097712 -name: vesicle targeting, trans-Golgi to periciliary membrane compartment -namespace: biological_process -def: "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces." [GOC:cilia, PMID:20106869, PMID:23351793, PMID:24814148, PMID:26485645, Reactome:R-HSA-5620920.1] -is_a: GO:0048199 ! vesicle targeting, to, from or within Golgi -relationship: part_of GO:0060271 ! cilium assembly -created_by: pr -creation_date: 2016-08-05T16:16:28Z - [Term] id: GO:0097734 name: extracellular exosome biogenesis @@ -6098,40 +5332,6 @@ intersection_of: GO:0099080 ! supramolecular complex intersection_of: bearer_of PATO:0015006 ! polymeric relationship: bearer_of PATO:0015006 ! polymeric -[Term] -id: GO:0099111 -name: microtubule-based transport -namespace: biological_process -def: "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194] -is_a: GO:0006810 ! transport -intersection_of: GO:0006810 ! transport -intersection_of: process_has_causal_agent GO:0005874 ! microtubule -relationship: process_has_causal_agent GO:0005874 ! microtubule - -[Term] -id: GO:0099512 -name: supramolecular fiber -namespace: cellular_component -alt_id: GO:0043205 -def: "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." [GOC:dos] -synonym: "fibril" RELATED [] -is_a: GO:0099081 ! supramolecular polymer -intersection_of: GO:0099080 ! supramolecular complex -intersection_of: bearer_of PATO:0002309 ! fiber shaped -intersection_of: bearer_of PATO:0015006 ! polymeric -relationship: bearer_of PATO:0002309 ! fiber shaped - -[Term] -id: GO:0099513 -name: polymeric cytoskeletal fiber -namespace: cellular_component -def: "A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits." [GOC:dos] -is_a: GO:0099512 ! supramolecular fiber -intersection_of: GO:0099512 ! supramolecular fiber -intersection_of: bearer_of PATO:0015006 ! polymeric -intersection_of: part_of GO:0005856 ! cytoskeleton -relationship: part_of GO:0005856 ! cytoskeleton - [Term] id: GO:0099536 name: synaptic signaling @@ -6154,17 +5354,6 @@ def: "Cell-cell signaling in either direction across the synaptic cleft." [GOC:d subset: goslim_synapse is_a: GO:0099536 ! synaptic signaling -[Term] -id: GO:0099568 -name: cytoplasmic region -namespace: cellular_component -def: "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm." [GOC:dos] -subset: gocheck_do_not_annotate -is_a: GO:0005737 ! cytoplasm -intersection_of: GO:0005737 ! cytoplasm -intersection_of: part_of GO:0005737 ! cytoplasm -relationship: part_of GO:0005737 ! cytoplasm - [Term] id: GO:0110165 name: cellular anatomical entity @@ -6236,17 +5425,6 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2017-03-23T14:44:23Z -[Term] -id: GO:0140056 -name: organelle localization by membrane tethering -namespace: biological_process -def: "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other." [PMID:27875684] -subset: goslim_pombe -is_a: GO:0022406 ! membrane docking -is_a: GO:0051640 ! organelle localization -created_by: pg -creation_date: 2017-06-27T09:58:51Z - [Term] id: GO:0140112 name: extracellular vesicle biogenesis @@ -6274,27 +5452,6 @@ relationship: has_target_start_location GO:0005622 ! intracellular anatomical st created_by: pg creation_date: 2019-05-22T11:20:45Z -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] -synonym: "organic molecular entity biosynthetic process" EXACT [] -synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] -synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] -synonym: "organic substance anabolism" EXACT [] -synonym: "organic substance biosynthesis" EXACT [] -synonym: "organic substance formation" EXACT [] -synonym: "organic substance synthesis" EXACT [] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-05T11:04:40Z - [Term] id: GO:1903047 name: mitotic cell cycle process @@ -6321,24 +5478,6 @@ intersection_of: part_of GO:0005576 ! extracellular region created_by: jl creation_date: 2014-10-22T14:26:11Z -[Term] -id: GO:1905349 -name: ciliary transition zone assembly -namespace: biological_process -def: "The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone." [GO_REF:0000079, GOC:cilia, GOC:TermGenie, PMID:21725307, PMID:23644468, PMID:24448408, PMID:26595381, PMID:26982032] -synonym: "cilial transition zone assembly" EXACT [GOC:TermGenie] -synonym: "cilial transition zone formation" EXACT [GOC:TermGenie] -synonym: "ciliary transition zone formation" EXACT [GOC:TermGenie] -synonym: "cilium transition zone assembly" EXACT [GOC:TermGenie] -synonym: "cilium transition zone formation" EXACT [GOC:TermGenie] -is_a: GO:0022607 ! cellular component assembly -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0035869 ! ciliary transition zone -relationship: part_of GO:0060271 ! cilium assembly -relationship: results_in_assembly_of GO:0035869 ! ciliary transition zone -created_by: pr -creation_date: 2016-08-04T14:49:43Z - [Term] id: GO:1990904 name: ribonucleoprotein complex @@ -6974,9 +6113,21 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z +[Term] +id: PATO:0002064 +name: fenestrated +namespace: quality +def: "A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes." [PATOC:me] +subset: cell_quality +subset: mpath_slim +subset: value_slim +is_a: PATO:0000141 ! structure +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X +creation_date: 2009-07-01T01:46:53Z + [Term] id: PATO:0002078 name: hollow @@ -6984,7 +6135,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6996,7 +6147,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -7007,7 +6158,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -7017,26 +6168,16 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z -[Term] -id: PATO:0002226 -name: subcylindrical -namespace: quality -def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] -subset: value_slim -is_a: PATO:0001873 ! cylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X -creation_date: 2010-07-13T04:22:30Z - [Term] id: PATO:0002266 name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -7049,20 +6190,9 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z -[Term] -id: PATO:0002309 -name: fiber shaped -namespace: quality -def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter." [PATOC:DC] -comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). -subset: value_slim -is_a: PATO:0002226 ! subcylindrical -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X -creation_date: 2011-09-09T04:50:10Z - [Term] id: PATO:0002318 name: superelliptic @@ -7070,7 +6200,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -7083,7 +6213,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -7093,7 +6223,7 @@ namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." [PATOC:WD] subset: value_slim is_a: PATO:0015008 ! distensibility -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:48:26Z [Term] @@ -7104,7 +6234,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X +property_value: terms:contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -7113,7 +6243,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -7175,6 +6305,9 @@ def: "An amino acid chain that is produced de novo by ribosome-mediated translat comment: The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB]. synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] +is_a: PR:000018263 ! amino acid chain +is_a: PR:000064867 ! protein-containing molecular entity +relationship: output_of GO:0006412 ! translation [Term] id: PR:000001002 @@ -7535,6 +6668,15 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein +[Term] +id: PR:000018263 +name: amino acid chain +namespace: protein +def: "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." [PRO:DAN, PRO:JSG] +comment: Category=polymer. +synonym: "peptide" NARROW [PRO:DAN] +synonym: "polypeptide" NARROW [PRO:DAN] + [Term] id: PR:000025796 name: integrin alpha @@ -7574,6 +6716,18 @@ comment: Category=family. synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] is_a: PR:000000001 ! protein +[Term] +id: PR:000064867 +name: protein-containing molecular entity +namespace: protein +def: "A molecular entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +synonym: "protein" NARROW [PRO:DAN] +synonym: "protein aggregate" NARROW [PRO:DAN] +synonym: "protein complex" NARROW [PRO:DAN] +synonym: "protein-containing complex" NARROW [PRO:DAN] +relationship: has_part PR:000000001 ! protein + [Term] id: UBERON:0000000 name: processual entity @@ -7621,7 +6775,7 @@ xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 -xref: FBbt:00007000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 @@ -7688,7 +6842,7 @@ relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0036295 ! renal pelvis/ureter relationship: RO:0002202 UBERON:0005081 {source="GO"} ! develops from ureter ureteric bud -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -7729,7 +6883,7 @@ relationship: part_of UBERON:0001556 ! lower urinary tract relationship: RO:0002150 UBERON:0001255 ! continuous with urinary bladder relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus relationship: RO:0002202 UBERON:0013241 {source="Wikipedia"} ! develops from embryonic urethral groove -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0000058 @@ -7742,7 +6896,7 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100314 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7788,7 +6942,7 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7975,10 +7129,10 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle relationship: RO:0002202 UBERON:0005749 ! develops from glomerular tuft relationship: RO:0002219 UBERON:0001230 ! surrounded by glomerular capsule -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:26:37Z [Term] @@ -8040,7 +7194,7 @@ xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure relationship: RO:0002202 UBERON:0002120 ! develops from pronephros -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI [Term] id: UBERON:0000081 @@ -8275,7 +7429,7 @@ xref: ZFS:0000045 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] @@ -8457,7 +7611,7 @@ relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0000165 @@ -8491,7 +7645,7 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -8515,7 +7669,7 @@ xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI [Term] @@ -8596,7 +7750,7 @@ intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -8619,7 +7773,7 @@ intersection_of: UBERON:0000468 ! multicellular organism intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] @@ -8684,11 +7838,11 @@ relationship: capable_of_part_of GO:0070295 ! renal water absorption relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -8748,7 +7902,7 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007019 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8783,7 +7937,7 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8811,7 +7965,7 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007016 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8836,7 +7990,7 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007015 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8873,7 +8027,7 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004856 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 @@ -8927,7 +8081,7 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8991,7 +8145,7 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007009 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -9027,7 +8181,7 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007013 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -9047,7 +8201,7 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group property_value: RO:0002175 NCBITaxon:33090 @@ -9074,7 +8228,7 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007003 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -9109,7 +8263,7 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -9142,7 +8296,7 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007005 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -9163,7 +8317,7 @@ relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000485 @@ -9182,7 +8336,7 @@ xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 -xref: FBbt:00007027 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007027 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 @@ -9194,7 +8348,7 @@ xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI [Term] id: UBERON:0000487 @@ -9223,7 +8377,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000489 @@ -9352,7 +8506,7 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000052 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism @@ -9373,7 +8527,7 @@ intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI [Term] @@ -9393,7 +8547,7 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000110 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -9427,7 +8581,7 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -9445,7 +8599,7 @@ xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -9465,7 +8619,7 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -9482,8 +8636,8 @@ xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -9509,7 +8663,7 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000126 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -9526,7 +8680,7 @@ xref: ZFA:0000041 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 [Term] @@ -9549,7 +8703,7 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000439 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -9562,7 +8716,7 @@ is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] @@ -9579,7 +8733,7 @@ synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 -xref: FBbt:00000123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00000123 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} @@ -9648,9 +8802,9 @@ relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002161 NCBITaxon:6239 property_value: RO:0002161 NCBITaxon:7227 property_value: RO:0002175 NCBITaxon:9606 @@ -9669,7 +8823,7 @@ is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: RO:0000086 PATO:0002124 ! has quality laminar -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] @@ -9754,7 +8908,7 @@ xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 -xref: FBbt:00004857 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004857 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 @@ -9783,10 +8937,10 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0022414 ! reproductive process relationship: has_part UBERON:0000991 ! gonad relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://purl.org/dc/terms/date "2022-06-10T18:22:34Z" xsd:dateTime -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI property_value: IAO:0000116 "consider splitting genitalia from reproductive system" xsd:string property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:date "2022-06-10T18:22:34Z" xsd:dateTime [Term] id: UBERON:0000991 @@ -9845,7 +8999,7 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005055 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9902,7 +9056,7 @@ xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 -xref: FBbt:00005056 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005056 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract @@ -9951,7 +9105,7 @@ disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002161 NCBITaxon:6073 property_value: RO:0002161 NCBITaxon:6157 @@ -9990,7 +9144,7 @@ xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0000383 ! musculature of body relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -10016,7 +9170,7 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -10044,8 +9198,8 @@ relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 property_value: RO:0002175 NCBITaxon:9606 @@ -10076,7 +9230,7 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -10115,7 +9269,7 @@ xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 -xref: FBbt:00005379 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005379 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 @@ -10126,7 +9280,7 @@ xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string [Term] @@ -10145,7 +9299,7 @@ xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 -xref: FBbt:00005383 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005383 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 @@ -10157,7 +9311,7 @@ xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string [Term] @@ -10175,7 +9329,7 @@ xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 -xref: FBbt:00005384 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005384 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 @@ -10188,7 +9342,7 @@ xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001045 ! midgut relationship: RO:0002202 UBERON:0003104 {source="Wikipedia"} ! develops from mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string [Term] @@ -10208,7 +9362,7 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005495 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -10255,7 +9409,7 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002202 UBERON:0005068 ! develops from neural rod -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -10271,7 +9425,7 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:10000000 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -10288,7 +9442,7 @@ property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001072 -name: posterior vena cava +name: inferior vena cava namespace: uberon def: "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Inferior_vena_cava] subset: human_reference_atlas @@ -10296,9 +9450,8 @@ subset: pheno_slim subset: uberon_slim synonym: "caudal vena cava" RELATED [VHOG:0001194] synonym: "inferior caval vein" EXACT [http://orcid.org/0000-0002-6601-2165] -synonym: "inferior vena cava" EXACT [Wikipedia:Venae_cavae] synonym: "postcava" RELATED [] -synonym: "posterior vena cava" EXACT [Wikipedia:Venae_cavae] +synonym: "posterior vena cava" EXACT [PMID:21154280] synonym: "vena cava inferior" RELATED OMO:0003011 [BTO:0002682, Wikipedia:Inferior_vena_cava] xref: AAO:0011083 xref: BTO:0002682 @@ -10320,7 +9473,7 @@ intersection_of: UBERON:0004087 ! vena cava intersection_of: RO:0002179 UBERON:0000154 ! drains posterior region of body relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10380,10 +9533,10 @@ is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: RO:0002179 UBERON:0002113 ! drains kidney relationship: RO:0002179 UBERON:0002113 ! drains kidney -relationship: RO:0002376 UBERON:0001072 ! tributary of posterior vena cava -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002376 UBERON:0001072 ! tributary of inferior vena cava +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10420,7 +9573,7 @@ relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter relationship: RO:0002150 UBERON:0000056 {source="FMA"} ! continuous with ureter relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10451,11 +9604,11 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10493,7 +9646,7 @@ relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10535,7 +9688,7 @@ relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} ! glomerular fi relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002202 UBERON:0004199 ! develops from S-shaped body relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI [Term] id: UBERON:0001231 @@ -10629,7 +9782,7 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00047153 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00047153 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -10645,8 +9798,8 @@ is_a: UBERON:0000161 ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001555 ! digestive tract relationship: RO:0002202 UBERON:0000931 ! develops from proctodeum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10690,9 +9843,9 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10751,7 +9904,7 @@ relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney relationship: RO:0002495 UBERON:0010532 {source="Bgee:AN"} ! immediate transformation of primitive nephron -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -10791,7 +9944,7 @@ relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerul relationship: RO:0002150 UBERON:0001290 ! continuous with proximal straight tubule relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI [Term] id: UBERON:0001288 @@ -10822,7 +9975,7 @@ intersection_of: RO:0002150 UBERON:0001292 ! continuous with distal convoluted t relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule relationship: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: IAO:0000116 "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string property_value: RO:0002175 NCBITaxon:8782 @@ -10847,7 +10000,7 @@ xref: Wikipedia:Descending_limb_of_loop_of_henle is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10911,7 +10064,7 @@ is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0004135 {source="EMAPA", source="GO", source="MA-modified-from-isa"} ! distal tubule relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10962,7 +10115,7 @@ xref: WBbt:0006919 is_a: UBERON:0000475 ! organism subdivision relationship: overlaps UBERON:0006866 ! terminal part of digestive tract relationship: RO:0002254 UBERON:0000931 ! has developmental contribution from proctodeum -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/507" xsd:anyURI [Term] @@ -11023,7 +10176,7 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney relationship: RO:0002252 UBERON:0009885 ! connecting branch of interlobar artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11048,7 +10201,7 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00003125 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 @@ -11198,7 +10351,7 @@ intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string [Term] @@ -11280,7 +10433,7 @@ is_a: UBERON:0003920 ! venous blood vessel is_a: UBERON:8410081 ! blood microvessel relationship: RO:0002176 UBERON:0001638 ! connects vein relationship: RO:0002176 UBERON:0001982 ! connects capillary -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11313,7 +10466,7 @@ intersection_of: RO:0002176 UBERON:0001982 ! connects capillary relationship: RO:0002176 UBERON:0001637 ! connects artery relationship: RO:0002176 UBERON:0001982 ! connects capillary relationship: RO:0002433 UBERON:0001637 ! contributes to morphology of artery -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI [Term] id: UBERON:0001981 @@ -11363,7 +10516,7 @@ relationship: part_of UBERON:0004537 ! blood vasculature relationship: RO:0000086 PATO:0002045 ! has quality dendritic relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11402,7 +10555,7 @@ intersection_of: RO:0002176 UBERON:0001979 ! connects venule intersection_of: RO:0002176 UBERON:0001980 ! connects arteriole relationship: RO:0002176 UBERON:0001979 ! connects venule relationship: RO:0002176 UBERON:0001980 ! connects arteriole -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string @@ -11452,7 +10605,7 @@ is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string property_value: RO:0002175 NCBITaxon:9606 @@ -11474,7 +10627,7 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00004208 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11553,9 +10706,9 @@ xref: XAO:0003192 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11662,7 +10815,7 @@ relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI @@ -11733,9 +10886,9 @@ relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2804-127X property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 +property_value: terms:contributor https://orcid.org/0000-0003-2804-127X [Term] id: UBERON:0002120 @@ -11872,8 +11025,8 @@ intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002303 @@ -11968,7 +11121,7 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005060 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12025,7 +11178,7 @@ relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499 relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12066,7 +11219,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] @@ -12129,8 +11282,8 @@ relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural pl relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12153,7 +11306,7 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00001057 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12351,7 +11504,7 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] @@ -12486,7 +11639,7 @@ relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme relationship: RO:0002202 UBERON:0000926 {source="XAO"} ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003068 @@ -12507,7 +11660,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003074 @@ -12538,7 +11691,7 @@ is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct relationship: RO:0002202 UBERON:0003060 ! develops from pronephric duct relationship: RO:0002202 UBERON:0005792 {source="EHDAA2"} ! develops from nephric ridge -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI property_value: IAO:0000116 "Consider adding subclasses for male and female specific variants" xsd:string property_value: IAO:0000116 "TODO - mesonephric portion of the nephric duct" xsd:string @@ -12575,7 +11728,7 @@ is_a: UBERON:0016879 ! future central nervous system relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -12606,7 +11759,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -12641,7 +11794,7 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -12691,7 +11844,7 @@ is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -12747,7 +11900,7 @@ intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] @@ -13014,7 +12167,7 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007474 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium @@ -13072,10 +12225,10 @@ xref: UMLS:C0042460 {source="ncithesaurus:Vena_Cava"} xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] id: UBERON:0004100 @@ -13092,7 +12245,7 @@ xref: SCTID:279371005 xref: Wikipedia:Collecting_duct_system is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002113 ! kidney -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13416,11 +12569,11 @@ xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000362 ! renal medulla relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13581,7 +12734,7 @@ is_a: UBERON:0000485 {source="EHDAA2"} ! simple columnar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI [Term] id: UBERON:0004535 @@ -13645,8 +12798,8 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: foaf:depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13740,7 +12893,7 @@ relationship: part_of UBERON:0001229 ! renal corpuscle relationship: RO:0002178 UBERON:0001285 ! supplies nephron relationship: RO:0002252 UBERON:0004723 ! connecting branch of interlobular artery relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13789,7 +12942,7 @@ xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel disjoint_from: UBERON:0009885 {source="Wikipedia:Renal_circulation"} ! interlobar artery relationship: RO:0002170 UBERON:0001552 ! connected to kidney arcuate artery -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13810,7 +12963,7 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -13965,7 +13118,7 @@ xref: Wikipedia:Somatopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000924 ! ectoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI [Term] id: UBERON:0004875 @@ -14027,7 +13180,7 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005811 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14043,7 +13196,7 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100315 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube @@ -14183,7 +13336,7 @@ xref: Wikipedia:Descending_limb_of_loop_of_Henle is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2276" xsd:string @@ -14205,7 +13358,7 @@ xref: Wikipedia:Connecting_tubule is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0012275 ! meso-epithelium relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -14479,7 +13632,7 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity @@ -14660,7 +13813,7 @@ intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: capable_of GO:0003094 ! glomerular filtration relationship: part_of UBERON:0004188 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! glomerular epithelium -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI [Term] id: UBERON:0005792 @@ -14712,7 +13865,7 @@ is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0011137 ! axial skeletal system relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI @@ -14741,7 +13894,7 @@ relationship: RO:0002202 UBERON:0004341 {source="Wikipedia"} ! develops from pri relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI [Term] id: UBERON:0006267 @@ -14979,7 +14132,7 @@ def: "The distalmost portion of the digestive tract, derived from the hindgut, a synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" NARROW [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] -xref: FBbt:00005756 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005756 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0005773 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: RO:0002150 UBERON:0001245 ! continuous with anus @@ -15311,7 +14464,7 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00005426 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15395,7 +14548,7 @@ relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex relationship: RO:0002202 UBERON:0010377 {source="PMID:21455939"} ! develops from mesenchyme from somatopleure relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region -property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string [Term] @@ -15548,7 +14701,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: RO:0002178 UBERON:0009913 ! supplies renal lobe relationship: RO:0002178 UBERON:0009913 ! supplies renal lobe -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -15582,7 +14735,7 @@ intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney -property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI property_value: IAO:0000116 "todo - add has_part relationships." xsd:string [Term] @@ -15594,7 +14747,7 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00100313 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular @@ -15731,8 +14884,8 @@ is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata relationship: RO:0002328 GO:0040011 ! functionally related to locomotion -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string +property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-04-23T10:46:51Z [Term] @@ -15836,7 +14989,7 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007330 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure @@ -16229,7 +15382,7 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +xref: FBbt:00007276 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure relationship: RO:0000086 PATO:0010001 ! has quality disconnected @@ -16382,8 +15535,8 @@ comment: It is quite common to refer to visceral muscles as smooth muscles, by a synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 -property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2023-02-16T10:17:46Z" xsd:dateTime [Typedef] id: BFO:0000067 @@ -17453,8 +16606,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17462,8 +16615,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 +property_value: terms:contributor https://orcid.org/0000-0003-1617-8244 +property_value: terms:contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17472,8 +16625,8 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 +property_value: terms:contributor https://orcid.org/0000-0001-9625-1899 +property_value: terms:contributor https://orcid.org/0000-0003-2620-0345 holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -17624,16 +16777,20 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon +is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon +is_transitive: true [Typedef] id: distally_connected_to @@ -17642,6 +16799,7 @@ namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to +inverse_of: proximally_connected_to ! proximally connected to [Typedef] id: ends_with @@ -17659,6 +16817,7 @@ id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] +is_symmetric: true is_a: RO:0002170 ! connected to [Typedef] @@ -17877,6 +17036,7 @@ namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] property_value: IAO:0000116 "add to RO" xsd:string holds_over_chain: RO:0002569 indirectly_supplies +is_transitive: true [Typedef] id: layer_part_of @@ -18335,18 +17495,21 @@ id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI +is_transitive: true [Typedef] id: trunk_part_of diff --git a/subsets/kidney_upper_slim.owl b/subsets/kidney_upper_slim.owl index d55f2848a..06b276c12 100644 --- a/subsets/kidney_upper_slim.owl +++ b/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-05-15 + + 2024-07-10 @@ -1044,6 +1044,12 @@ WHERE { + + + + + + @@ -4511,6 +4517,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + carries uberon channel_for @@ -4522,6 +4530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_from channels_from @@ -4532,6 +4541,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon channels_into channels_into @@ -4544,6 +4554,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -4562,6 +4573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -4591,6 +4603,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4699,6 +4712,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -4710,6 +4724,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_distally_connected_to transitively distally connected to @@ -4721,6 +4736,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + uberon transitively_proximally_connected_to transitively proximally connected to @@ -5504,49 +5520,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A cell that has a filiform extrusion of the cell surface. - VHOG:0001532 - XAO:0000031 - ZFA:0009032 - - ciliated cell - - - - - A cell that has a filiform extrusion of the cell surface. - GOC:tfm - - - - - ZFA:0009032 - - - - - @@ -5596,43 +5569,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - An epithelial cell that has a cilia. - FMA:70605 - ZFA:0009035 - - ciliated epithelial cell - - - - - An epithelial cell that has a cilia. - GOC:tfm - - - - - ZFA:0009035 - - - - - @@ -5680,15 +5616,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - @@ -5705,17 +5640,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that lines the vasculature. ZFA:0009036 - cuboidal endothelial cell of vascular tree blood vessel endothelial cell - - - - - true - @@ -5841,7 +5769,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 @@ -6477,23 +6410,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - ZFA:0009143 - brush border epithelial cell - - - - - ZFA:0009143 - - - - - @@ -8009,12 +7925,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + + + + + + + + + + + + + + + + + + + An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. ZFA:0009286 window cell - fenestrated cell + fenestrated endothelial cell + + + + An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. + DOI:10.1007/978-3-211-99390-3_133 + @@ -8754,7 +8694,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. - 2010-01-06T03:43:20Z + 2010-01-06T03:43:20Z hematopoietic lineage restricted progenitor cell @@ -8797,7 +8737,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. - 2010-01-06T03:43:27Z + 2010-01-06T03:43:27Z This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell @@ -8836,7 +8776,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell derived from ectoderm. - 2010-06-29T03:38:22Z + 2010-06-29T03:38:22Z FMA:69074 ZFA:0009385 ecto-epithelial cell @@ -8880,7 +8820,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Epithelial cell derived from mesoderm or mesenchyme. - 2010-06-29T03:49:14Z + 2010-06-29T03:49:14Z FMA:69076 ZFA:0009388 epithelial mesenchymal cell @@ -8908,7 +8848,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. - 2010-08-24T02:06:40Z + 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 @@ -8954,7 +8894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. - 2010-08-25T02:20:55Z + 2010-08-25T02:20:55Z FMA:84143 KUPO:0001033 Goormaghtigh cell @@ -8993,24 +8933,23 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + + + + + + An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. - 2010-08-26T10:59:44Z + 2010-08-26T10:59:44Z BTO:0004632 FMA:70970 glomerular endothelial cell - - - - - true - @@ -9044,7 +8983,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell containing at least one nucleus. - 2010-09-07T03:32:33Z + 2010-09-07T03:32:33Z FMA:67513 nucleate cell @@ -9117,7 +9056,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -9135,6 +9073,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions. epithelial cell of proximal tubule @@ -9176,7 +9115,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of the nervous system. - 2010-09-15T01:34:57Z + 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 @@ -9215,7 +9154,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. - 2010-09-15T03:01:54Z + 2010-09-15T03:01:54Z CALOHA:TS-2096 FMA:63875 MESH:D003239 @@ -9245,7 +9184,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the embryo. - 2010-09-15T03:39:21Z + 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 WBbt:0007028 @@ -9290,7 +9229,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell located in the heart, including both muscle and non muscle cells. - 2010-12-07T09:37:22Z + 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 @@ -9326,7 +9265,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell of the kidney. - 2011-02-08T10:46:34Z + 2011-02-08T10:46:34Z KUPO:0001019 ZFA:0009374 @@ -9360,7 +9299,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial progenitor cell that participates in angiogenesis during development. - 2011-02-28T04:20:39Z + 2011-02-28T04:20:39Z ZFA:0005773 See CL:0002619. embryonic blood vessel endothelial progenitor cell @@ -9444,7 +9383,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell that is part of a cortex of kidney. - 2011-10-25T03:49:41Z + 2011-10-25T03:49:41Z kidney cortical cell @@ -9493,7 +9432,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. - 2012-06-27T08:27:35Z + 2012-06-27T08:27:35Z ZFA:0007084 premigratory neural crest cell @@ -9765,7 +9704,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. - 2009-12-22T04:23:25Z + 2009-12-22T04:23:25Z eosinophilic acidophilic cytoplasm @@ -9801,7 +9740,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. - 2009-12-22T04:24:54Z + 2009-12-22T04:24:54Z basophilic cytoplasm @@ -9836,7 +9775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. - 2009-12-28T04:25:23Z + 2009-12-28T04:25:23Z polychromatophilic cytoplasm @@ -10321,12 +10260,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney corpuscule cell - - - - - true - @@ -10484,12 +10417,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different KUPO:0001036 glomerular cell - - - - - true - @@ -10602,7 +10529,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - @@ -11011,59 +10937,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. - https://github.com/geneontology/go-ontology/issues/23114 - https://github.com/geneontology/go-ontology/issues/23195 - microtubule cytoskeleton organisation - biological_process - microtubule cytoskeleton organization and biogenesis - GO:0000226 - - microtubule cytoskeleton organization - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins. - GOC:mah - - - - - microtubule cytoskeleton organisation - GOC:mah - - - - - microtubule cytoskeleton organization and biogenesis - GOC:mah - - - - @@ -11116,7 +10989,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent. GOC:mah ISBN:0815316194 - Reactome:69278 @@ -11240,37 +11112,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - A process that results in a parallel arrangement of microtubules. - microtubule bundling - biological_process - GO:0001578 - microtubule bundle formation - - - - - A process that results in a parallel arrangement of microtubules. - GOC:dph - - - - @@ -12321,32 +12162,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12652,132 +12493,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. - Wikipedia:Vacuole - cellular_component - vacuolar carboxypeptidase Y - GO:0005773 - - - - - - - - - - - - - vacuole - - - - - A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. - GOC:mtg_sensu - ISBN:0198506732 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. - Golgi - NIF_Subcellular:sao451912436 - Wikipedia:Golgi_apparatus - Golgi complex - Golgi ribbon - cellular_component - GO:0005794 - - - - - - - - - - - - Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. - Golgi apparatus - - - - - A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways. - ISBN:0198506732 - - - - - - - - - Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. - NIF_Subcellular:sao819927218 - cellular_component - Golgi vesicle - vesicular component - GO:0005798 - Note that this definition includes vesicles that are transiently associated with the Golgi. - Golgi-associated vesicle - - - - - Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell. - GOC:mah - - - - - vesicular component - NIF_Subcellular:sao138219748 - - - - @@ -12837,76 +12552,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. - Wikipedia:Cytoskeleton - cellular_component - GO:0005856 - - - - - - - - - - - - - - cytoskeleton - - - - - A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. - GOC:mah - PMID:16959967 - PMID:27419875 - - - - - - - - - - - - - - - Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. - NIF_Subcellular:sao1846835077 - Wikipedia:Microtubule - microtubuli - microtubulus - neurotubule - cellular_component - GO:0005874 - - microtubule - - - - - Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. - ISBN:0879693568 - - - - - neurotubule - NIF_Subcellular:sao248349196 - - - - @@ -13005,116 +12650,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. - - - - - - - GO:0072372 - FMA:67181 - NIF_Subcellular:sao787716553 - Wikipedia:Cilium - eukaryotic flagellum - microtubule-based flagellum - primary cilium - cellular_component - flagellum - GO:0005929 - - - - - Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. - cilium - - - - - A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. - GOC:cilia - GOC:curators - GOC:kmv - GOC:vw - ISBN:0198547684 - PMID:16824949 - PMID:17009929 - PMID:20144998 - - - - - - - - - - - - - - - - - - - - - - - - - - - The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GO:0035085 - GO:0035086 - Wikipedia:Axoneme - ciliary axoneme - cilium axoneme - flagellar axoneme - flagellum axoneme - cellular_component - GO:0005930 - - Note that cilia and eukaryotic flagella are deemed to be equivalent. In diplomonad species, such as Giardia, the axoneme may extend intracellularly up to 5um away from the plane of the plasma membrane. - axoneme - - - - - The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GOC:bf - GOC:cilia - ISBN:0198547684 - - - - @@ -13351,37 +12886,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. - biological_process - GO:0006903 - vesicle targeting - - - - - The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo. - GOC:mah - PMID:17335816 - - - - @@ -13595,123 +13099,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. - cytoskeleton organisation - biological_process - cytoskeletal organization and biogenesis - cytoskeletal regulator activity - cytoskeleton organization and biogenesis - GO:0007010 - - - - - - - cytoskeleton organization - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures. - GOC:dph - GOC:jl - GOC:mah - - - - - cytoskeletal organization and biogenesis - GOC:mah - - - - - cytoskeleton organization and biogenesis - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. - https://github.com/geneontology/go-ontology/issues/19809 - biological_process - GO:0007017 - - microtubule-based process - - - - - Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins. - GOC:mah - - - - - - - - - A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - biological_process - GO:0007018 - - - microtubule-based movement - - - - - A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - GOC:cjm - ISBN:0815316194 - - - - @@ -14461,7 +13848,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. https://github.com/geneontology/go-ontology/issues/15249 https://github.com/geneontology/go-ontology/issues/25418 @@ -14828,56 +14214,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. - tb - 2009-05-27T10:56:08Z - microtubule-based transport - establishment of localization by movement along microtubule - movement along microtubule - biological_process - GO:0010970 - transport along microtubule - - - - - The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity. - GOC:dph - GOC:mah - GOC:tb - - - - - establishment of localization by movement along microtubule - GOC:dph - - - - @@ -14934,46 +14270,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. - Wikipedia:Endomembrane_system - cellular_component - GO:0012505 - - - - endomembrane system - - - - - A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. - GOC:lh - - - - @@ -14988,8 +14284,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different + - The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport @@ -15009,25 +14305,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. - cellular_component - GO:0015630 - microtubule cytoskeleton - - - - - The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins. - GOC:jl - ISBN:0395825172 - - - - @@ -15225,64 +14502,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. - https://github.com/geneontology/go-ontology/issues/25421 - GO:0006899 - vesicle transport - vesicular transport - nonselective vesicle transport - biological_process - protein sorting along secretory pathway - vesicle trafficking - GO:0016192 - - - - - - - - vesicle-mediated transport - - - - - A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. - GOC:ai - GOC:mah - ISBN:08789310662000 - - - - - vesicular transport - GOC:mah - - - - @@ -15575,26 +14794,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere. - biological_process - GO:0022406 - - membrane docking - - - - - The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere. - GOC:isa_complete - PMID:27875684 - - - - @@ -15960,7 +15159,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -16012,7 +15211,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl GOC:mah - http://www.cogsci.princeton.edu/~wn/ + PMID:18391171 @@ -16047,7 +15246,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0198506732 PMID:26820516 PMID:28096264 - http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html @@ -16416,76 +15614,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. - biological_process - GO:0030705 - - - cytoskeleton-dependent intracellular transport - - - - - The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell. - GOC:mah - - - - - - - - - - - - - - - A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. - intraflagellar transport complex - intraflagellar transport particle - cellular_component - IFT complex - GO:0030990 - - Note that we deem cilia and microtubule-based flagella to be equivalent. - intraciliary transport particle - - - - - A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. - GOC:cilia - GOC:kmv - PMID:14570576 - PMID:22118932 - PMID:23945166 - - - - @@ -16522,110 +15650,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A vesicle found in the cytoplasm of a cell. - GO:0016023 - NIF_Subcellular:sao180601769 - cellular_component - cytoplasmic membrane bounded vesicle - cytoplasmic membrane-enclosed vesicle - cytoplasmic, membrane-bounded vesicle - GO:0031410 - - - - - - - cytoplasmic vesicle - - - - - A vesicle found in the cytoplasm of a cell. - GOC:ai - GOC:mah - GOC:vesicles - - - - - - - - - - - - - - - - - - - - - - - - - - A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. - https://github.com/geneontology/go-ontology/issues/22021 - GO:0034629 - establishment and maintenance of protein complex localization - protein complex localisation - biological_process - cellular protein complex localisation - cellular protein complex localization - cellular protein-containing complex localization - establishment and maintenance of cellular protein complex localization - protein complex localization - GO:0031503 - protein-containing complex localization - - - - - A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location. - GOC:mah - - - - - protein complex localisation - GOC:mah - - - - - cellular protein complex localisation - GOC:mah - - - - @@ -16856,42 +15880,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. - cellular_component - GO:0032838 - plasma membrane bounded cell projection cytoplasm - - - - - All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. - GOC:krc - GOC:mah - - - - @@ -17049,55 +16037,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A process in which a protein is transported to, or maintained in, a location within an organelle. - protein localisation to organelle - protein localization in organelle - biological_process - GO:0033365 - protein localization to organelle - - - - - A process in which a protein is transported to, or maintained in, a location within an organelle. - GOC:mah - - - - - protein localisation to organelle - GOC:mah - - - - - protein localization in organelle - GOC:mah - - - - @@ -17181,72 +16120,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GO:0035083 - GO:0035084 - ciliary axoneme assembly - cilium axoneme assembly - flagellar axoneme assembly - flagellum axoneme assembly - biological_process - axoneme biogenesis - cilium axoneme biogenesis - GO:0035082 - Note that cilia and eukaryotic flagella are deemed to be equivalent. - axoneme assembly - - - - - The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements. - GOC:bf - GOC:cilia - GOC:jl - ISBN:0815316194 - - - - - axoneme biogenesis - GOC:mah - - - - - cilium axoneme biogenesis - GOC:mah - - - - @@ -17428,81 +16301,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. - bf - 2011-03-17T10:55:42Z - intraflagellar transport - Reactome:R-HSA-5620924.2 - biological_process - intraciliary transport involved in cilium morphogenesis - intraflagellar transport involved in cilium morphogenesis - GO:0035735 - intraciliary transport involved in cilium assembly - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly. - GOC:bf - GOC:cilia - Reactome:R-HSA-5620924.2 - - - - - - - - - - - - - - - A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. - bf - 2011-05-25T03:09:58Z - cilial transition zone - cilium transition zone - cellular_component - connecting cilium - GO:0035869 - Depending on the species, this region may have a distinct geometrically shaped electron-dense structure within the axonemal lumen visible in electron microscopy images; most animals don't display this inner structure. The axoneme extends through the ciliary transition zone, but only consists of the outer doublets. The central pair, axonemal spokes, and dynein complexes are not found in this part of the ciliary shaft. Note that the connecting cilium of the photoreceptor cells is thought to be equivalent to the transition zone. - ciliary transition zone - - - - - A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm. - GOC:cilia - GOC:kmv - PMID:21422230 - - - - @@ -17568,86 +16366,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. - - - - - - - GO:0035734 - Wikipedia:Intraflagellar_transport - intraflagellar transport - intraflagellar transport involved in cilium organization - intraflagellar transport involved in microtubule-based flagellum organisation - biological_process - IFT - GO:0042073 - Note that we deem cilium and microtubule-based flagellum to be equivalent. - intraciliary transport - - - - - The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins. - GOC:cilia - GOC:kmv - PMID:17981739 - PMID:18180368 - PMID:22869374 - Reactome:R-HSA-5620924.2 - - - - @@ -17735,7 +16453,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl - http://www.cogsci.princeton.edu/~wn/ + PMID:16318917 @@ -18278,6 +16996,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. https://github.com/geneontology/go-ontology/issues/26424 + Wikipedia:Primary_metabolite primary metabolism biological_process GO:0044238 @@ -18293,7 +17012,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators - http://www.metacyc.org @@ -18324,61 +17042,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - jl - 2013-03-27T15:09:58Z - microtubule-based flagellum organization - biological_process - GO:0044782 - - - Note that we deem cilium and microtubule-based flagellum to be equivalent. - cilium organization - - - - - A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - GOC:cilia - GOC:jl - - - - @@ -18484,54 +17147,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances within a cell. - jl - 2013-12-18T14:04:50Z - GO:1902582 - biological_process - single organism intracellular transport - single-organism intracellular transport - GO:0046907 - intracellular transport - - - - - The directed movement of substances within a cell. - GOC:ai - - - - - single organism intracellular transport - GOC:TermGenie - - - - @@ -18569,102 +17184,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. - biological_process - Golgi-derived vesicle transport - GO:0048193 - - Golgi vesicle transport - - - - - The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles. - GOC:jid - ISBN:0716731363 - PMID:10219233 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. - Golgi vesicle targeting - dictyosome vesicle targeting - vesicle targeting, to, from or within dictyosome - biological_process - GO:0048199 - vesicle targeting, to, from or within Golgi - - - - - The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation. - GOC:jid - GOC:mah - ISBN:0716731363 - PMID:10219233 - - - - @@ -19616,63 +18135,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process in which an organelle is transported to, and/or maintained in, a specific location. - https://github.com/geneontology/go-ontology/issues/19809 - establishment and maintenance of organelle localization - organelle localisation - biological_process - GO:0051640 - - organelle localization - - - - - Any process in which an organelle is transported to, and/or maintained in, a specific location. - GOC:ai - - - - - organelle localisation - GOC:mah - - - - @@ -19719,199 +18181,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - cytoplasmic vesicle localization - establishment and maintenance of vesicle localization - vesicle localisation - biological_process - GO:0051648 - vesicle localization - - - - - Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location. - GOC:ai - - - - - vesicle localisation - GOC:mah - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. - establishment of localisation in cell - establishment of intracellular localization - establishment of localization within cell - positioning within cell - biological_process - establishment of cellular localization - GO:0051649 - establishment of localization in cell - - - - - Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. - GOC:ai - GOC:dos - GOC:dph - GOC:tb - - - - - establishment of localisation in cell - GOC:mah - - - - - establishment of cellular localization - GOC:dph - GOC:tb - - - - - - - - - - - - - - - - - - - - - - The directed movement of a vesicle to a specific location. - establishment of vesicle localisation - biological_process - GO:0051650 - establishment of vesicle localization - - - - - The directed movement of a vesicle to a specific location. - GOC:ai - - - - - establishment of vesicle localisation - GOC:mah - - - - - - - - - - - - - - - - - - - - - The directed movement of an organelle to a specific location. - establishment of organelle localisation - biological_process - GO:0051656 - establishment of organelle localization - - - - - The directed movement of an organelle to a specific location. - GOC:ai - - - - - establishment of organelle localisation - GOC:mah - - - - @@ -20005,121 +18274,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - - - - - - - GO:0042384 - Reactome:R-HSA-5617833.2 - ciliogenesis - cilium formation - microtubule-based flagellum assembly - biological_process - cilium biogenesis - cilium morphogenesis - cilium organization - GO:0060271 - Note that we deem cilium and microtubule-based flagellum to be equivalent. - cilium assembly - - - - - The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. - GOC:BHF - GOC:cilia - GOC:dph - GOC:kmv - GOC:pr - GOC:vw - ISBN:0198506732 - PMID:13978319 - PMID:27350441 - Reactome:R-HSA-5617833.2 - - - - - cilium biogenesis - GOC:mah - - - - - cilium organization - GOC:dph - - - - @@ -20216,61 +18370,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process in which a protein is transported to, or maintained in, a location within a cilium. - - - - - - - dph - 2013-03-22T15:41:44Z - biological_process - GO:0061512 - protein localization to cilium - - - - - A process in which a protein is transported to, or maintained in, a location within a cilium. - GOC:dph - - - - @@ -20727,51 +18826,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. - mah - 2010-03-08T02:15:14Z - biological_process - GO:0071702 - organic substance transport - - - - - The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. - GOC:mah - - - - - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - mah - 2010-03-08T03:32:18Z - organic molecular entity metabolic process - organic molecular entity metabolism - organic substance metabolism - biological_process - GO:0071704 - - organic substance metabolic process - - - - - The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. - GOC:mah - - - - @@ -20992,55 +19046,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. - pr - 2011-03-23T01:52:31Z - cilium plasm - microtubule-based flagellar matrix - microtubule-based flagellum matrix - cellular_component - cilial cytoplasm - ciliary cytoplasm - cilium cytoplasm - microtubule-based flagellar cytoplasm - microtubule-based flagellum cytoplasm - GO:0097014 - Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". - ciliary plasm - - - - - All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. - GOC:BHF - GOC:cilia - GOC:dos - PMID:17895364 - - - - @@ -21157,139 +19162,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - An arrangement of closely apposed microtubules running parallel to each other. - pr - 2012-11-07T15:01:27Z - NIF_Subcellular:sao1872343973 - microtubule fascicle - cellular_component - GO:0097427 - microtubule bundle - - - - - An arrangement of closely apposed microtubules running parallel to each other. - NIF_Subcellular:sao1872343973 - - - - - - - - - - - - - - - - - - - - - Any vesicle that is part of the intracellular region. - pr - 2016-03-29T17:39:45Z - cellular_component - GO:0097708 - intracellular vesicle - - - - - Any vesicle that is part of the intracellular region. - GOC:vesicles - - - - - - - - - - - - - - - The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane. - pr - 2016-08-05T16:12:33Z - Reactome:R-HSA-5620912.1 - ciliary basal body docking - biological_process - anchoring of the basal body to the plasma membrane - GO:0097711 - Basal bodies in jawed vertebrates appear to first attach to a ciliary vesicle. It is unclear how specific this is to jawed vertebrates or if other organisms also employ this sequence. Some species like Giardia intestinalis do not relocate their basal bodies to the plasma membrane, but have their axonemes extend through the cytosol to then protrude out of the cell to form flagella. - ciliary basal body-plasma membrane docking - - - - - The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane. - GOC:cilia - PMID:13978319 - PMID:23348840 - PMID:23530209 - PMID:25686250 - PMID:26981235 - Reactome:R-HSA-5620912.1 - - - - - - - - - - - - - - - The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. - pr - 2016-08-05T16:16:28Z - biological_process - GO:0097712 - vesicle targeting, trans-Golgi to periciliary membrane compartment - - - - - The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces. - GOC:cilia - PMID:20106869 - PMID:23351793 - PMID:24814148 - PMID:26485645 - Reactome:R-HSA-5620920.1 - - - - @@ -21689,122 +19561,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - biological_process - GO:0099111 - microtubule-based transport - - - - - A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules. - GOC:cjm - ISBN:0815316194 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GO:0043205 - cellular_component - fibril - GO:0099512 - supramolecular fiber - - - - - A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. - GOC:dos - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. - cellular_component - GO:0099513 - polymeric cytoskeletal fiber - - - - - A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits. - GOC:dos - - - - @@ -21873,42 +19629,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. - cellular_component - GO:0099568 - - cytoplasmic region - - - - - Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. - GOC:dos - - - - @@ -22095,28 +19815,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other. - pg - 2017-06-27T09:58:51Z - biological_process - GO:0140056 - - organelle localization by membrane tethering - - - - - The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other. - PMID:27875684 - - - - @@ -22188,63 +19886,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - https://github.com/geneontology/go-ontology/issues/26424 - pr - 2012-11-05T11:04:40Z - organic molecular entity anabolism - organic molecular entity biosynthesis - organic molecular entity biosynthetic process - organic molecular entity formation - organic molecular entity synthesis - organic substance anabolism - organic substance biosynthesis - organic substance formation - organic substance synthesis - biological_process - GO:1901576 - - organic substance biosynthetic process - - - - - The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. - GOC:TermGenie - GOC:pr - - - - - organic molecular entity anabolism - GOC:TermGenie - - - - - organic molecular entity biosynthesis - GOC:TermGenie - - - - - organic molecular entity formation - GOC:TermGenie - - - - - organic molecular entity synthesis - GOC:TermGenie - - - - @@ -22327,91 +19968,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. - pr - 2016-08-04T14:49:43Z - cilial transition zone assembly - cilial transition zone formation - ciliary transition zone formation - cilium transition zone assembly - cilium transition zone formation - biological_process - GO:1905349 - ciliary transition zone assembly - - - - - The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone. - GOC:TermGenie - GOC:cilia - GO_REF:0000079 - PMID:21725307 - PMID:23644468 - PMID:24448408 - PMID:26595381 - PMID:26982032 - - - - - cilial transition zone assembly - GOC:TermGenie - - - - - cilial transition zone formation - GOC:TermGenie - - - - - ciliary transition zone formation - GOC:TermGenie - - - - - cilium transition zone assembly - GOC:TermGenie - - - - - cilium transition zone formation - GOC:TermGenie - - - - @@ -23883,6 +21439,29 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes. + + 2009-07-01T01:46:53Z + quality + PATO:0002064 + + + + fenestrated + + + + + A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes. + PATOC:me + + + + @@ -23970,27 +21549,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. - - 2010-07-13T04:22:30Z - quality - PATO:0002226 - - subcylindrical - - - - - A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. - url:http://www.thefreedictionary.com/Subcylindrical - - - - @@ -24035,28 +21593,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. - - 2011-09-09T04:50:10Z - quality - PATO:0002309 - - Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). - fiber shaped - - - - - A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. - PATOC:DC - - - - @@ -24275,6 +21811,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein @@ -25226,6 +22770,39 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + peptide + polypeptide + protein + PR:000018263 + Category=polymer. + amino acid chain + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + PRO:DAN + PRO:JSG + + + + + peptide + PRO:DAN + + + + + polypeptide + PRO:DAN + + + + @@ -25357,6 +22934,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + A molecular entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein + PR:000064867 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). + protein-containing molecular entity + + + + + A molecular entity that minimally consists of a protein. + PRO:DAN + + + + + protein + PRO:DAN + + + + + protein aggregate + PRO:DAN + + + + + protein complex + PRO:DAN + + + + + protein-containing complex + PRO:DAN + + + + @@ -25552,7 +23181,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25606,14 +23235,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -25663,7 +23292,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25711,14 +23340,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -26225,7 +23854,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26275,14 +23904,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -26545,14 +24174,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -26584,24 +24213,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different metanephros - + - + - + GO - + ISBN:9780878932504 @@ -26716,8 +24345,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -26741,11 +24370,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureteric bud - + - + @@ -26758,13 +24387,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 - + ISBN:9780878932504 @@ -27145,7 +24774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27181,14 +24810,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -27448,8 +25077,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -27475,24 +25104,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -27533,8 +25162,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -27552,24 +25181,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -27592,7 +25221,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27631,14 +25260,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -27920,15 +25549,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -27965,34 +25594,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -29334,7 +26963,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29376,14 +27005,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -29741,7 +27370,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29776,14 +27405,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different abdomen - + - + MA @@ -30012,7 +27641,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -30047,14 +27676,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -30094,7 +27723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -30129,14 +27758,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -30177,7 +27806,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -30218,14 +27847,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -30391,7 +28020,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30434,7 +28063,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -30447,7 +28076,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -30509,7 +28138,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30581,14 +28210,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -31442,7 +29071,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31492,14 +29121,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -31565,7 +29194,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -31610,7 +29239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -31624,7 +29253,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -31821,7 +29450,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31855,14 +29484,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -32142,7 +29771,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different XAO:0000388 galen:InferiorVenaCava inferior caval vein - inferior vena cava posterior vena cava uberon caudal vena cava @@ -32152,7 +29780,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - posterior vena cava + inferior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png @@ -32174,17 +29802,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different inferior caval vein http://orcid.org/0000-0002-6601-2165 - - - - inferior vena cava - Wikipedia:Venae_cavae - posterior vena cava - Wikipedia:Venae_cavae + PMID:21154280 @@ -32360,14 +29982,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32419,24 +30041,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -32482,7 +30104,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32518,14 +30140,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -32561,7 +30183,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32606,14 +30228,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -32687,7 +30309,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32729,14 +30351,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -32826,10 +30448,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32873,7 +30495,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron tubule - + @@ -32882,14 +30504,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + GO MA ZFA @@ -32903,7 +30525,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -33117,7 +30739,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33164,7 +30786,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -33177,7 +30799,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -33307,7 +30929,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33320,7 +30942,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -33351,24 +30973,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -33419,14 +31041,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33462,11 +31084,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -33479,13 +31101,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GO - + Wikipedia @@ -33617,7 +31239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33644,7 +31266,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -33657,7 +31279,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -33681,14 +31303,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33727,11 +31349,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal straight tubule - + - + @@ -33744,13 +31366,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + MA - + MA @@ -33792,7 +31414,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33828,7 +31450,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -33841,7 +31463,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EMAPA GO MA-modified-from-isa @@ -34116,7 +31738,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34139,14 +31761,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -34187,7 +31809,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -34224,14 +31846,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -34867,8 +32489,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -34881,7 +32503,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34935,34 +32557,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35819,7 +33441,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35871,14 +33493,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney - + - + FMA @@ -35913,8 +33535,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -35952,11 +33574,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -35969,13 +33591,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + ZFA @@ -36302,7 +33924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36321,7 +33943,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -36343,24 +33965,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different juxtaglomerular apparatus - + - + - + MA - + GO @@ -36484,8 +34106,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -36502,24 +34124,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -36661,9 +34283,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -36711,15 +34333,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -36738,19 +34360,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36790,8 +34412,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -36829,11 +34451,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -36846,13 +34468,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -36912,8 +34534,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -36931,24 +34553,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different macula densa - + - + - + MA - + GO @@ -36973,22 +34595,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37021,45 +34643,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37423,7 +35045,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37476,14 +35098,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -37701,7 +35323,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -37724,14 +35346,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -37772,8 +35394,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -37792,11 +35414,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -37809,13 +35431,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Wikipedia - + XAO @@ -37921,9 +35543,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -37962,34 +35584,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -38098,7 +35720,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -38127,7 +35749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -38140,7 +35762,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -38194,9 +35816,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38225,34 +35847,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38292,7 +35914,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38318,7 +35940,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38331,7 +35953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -38378,7 +36000,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38418,7 +36040,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38431,7 +36053,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -38481,15 +36103,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -38506,15 +36128,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -38527,19 +36149,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -38568,8 +36190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -38593,11 +36215,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -38616,13 +36238,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -38867,7 +36489,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38893,14 +36515,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -39588,7 +37210,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -39603,14 +37225,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -40190,8 +37812,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -40208,24 +37830,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal tubule - + - + - + GO - + GO @@ -40284,7 +37906,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -40294,14 +37916,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004136 intermediate tubule - + - + FMA @@ -40377,8 +37999,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -40390,24 +38012,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -40460,7 +38082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -40479,14 +38101,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -40708,8 +38330,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -40719,24 +38341,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different comma-shaped body - + - + - + cjm - + ZFA @@ -40758,8 +38380,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -40771,24 +38393,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different S-shaped body - + - + - + cjm - + GO @@ -41200,7 +38822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41238,14 +38860,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -41785,7 +39407,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41822,14 +39444,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -42189,7 +39811,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42203,14 +39825,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -42237,7 +39859,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42276,14 +39898,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -42581,7 +40203,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42602,14 +40224,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -42675,9 +40297,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -42697,34 +40319,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -43199,7 +40821,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -43207,14 +40829,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005095 kidney rudiment - + - + GO @@ -43330,7 +40952,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -43348,14 +40970,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -44086,7 +41708,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44102,14 +41724,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -44226,7 +41848,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44244,14 +41866,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -44279,7 +41901,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44306,7 +41928,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different gonad primordium - + @@ -44319,7 +41941,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -44378,14 +42000,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -44403,24 +42025,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -44467,7 +42089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44484,14 +42106,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular tuft - + - + Wikipedia @@ -44741,7 +42363,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44769,14 +42391,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -44861,7 +42483,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44871,7 +42493,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -44890,7 +42512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -44987,7 +42609,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45026,14 +42648,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -45067,7 +42689,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -45081,7 +42703,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -45094,7 +42716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45122,7 +42744,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -45139,14 +42761,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45690,7 +43312,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -45700,14 +43322,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0006853 renal cortex tubule - + - + MA @@ -46379,7 +44001,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46405,7 +44027,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -46421,7 +44043,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -46582,7 +44204,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46590,7 +44212,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -46603,7 +44225,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -46817,7 +44439,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46834,14 +44456,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -46979,7 +44601,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47017,14 +44639,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -47077,7 +44699,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -47088,7 +44710,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0008987 renal parenchyma - + @@ -47101,7 +44723,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -47171,7 +44793,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47188,14 +44810,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47314,7 +44936,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47322,14 +44944,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47428,7 +45050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47438,14 +45060,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -47766,7 +45388,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47784,14 +45406,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010227 future cardiac atrium - + - + ZFA @@ -47934,7 +45556,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47948,7 +45570,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010377 mesenchyme from somatopleure - + @@ -47961,7 +45583,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -47977,7 +45599,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -47987,14 +45609,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -48027,7 +45649,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48043,7 +45665,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010532 primitive nephron - + @@ -48056,7 +45678,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -48072,7 +45694,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48083,7 +45705,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010536 nephron progenitor - + @@ -48096,7 +45718,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -48339,8 +45961,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -48352,11 +45974,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -48369,13 +45991,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -48436,7 +46058,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48446,7 +46068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48459,7 +46081,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -48483,7 +46105,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48508,14 +46130,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different upper urinary tract - + - + FMA @@ -48833,7 +46455,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48848,14 +46470,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -48878,20 +46500,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -48901,20 +46523,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -48941,7 +46563,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -48961,14 +46583,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeleton of pelvic complex - + - + FMA @@ -49020,7 +46642,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -49031,14 +46653,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -49609,7 +47231,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -49632,7 +47254,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -49645,7 +47267,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -50056,7 +47678,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -50067,14 +47689,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis/ureter - + - + NCIT @@ -50419,5 +48041,5 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + diff --git a/subsets/kidney_upper_slim.tsv b/subsets/kidney_upper_slim.tsv index 1147052a5..684848508 100644 --- a/subsets/kidney_upper_slim.tsv +++ b/subsets/kidney_upper_slim.tsv @@ -1,364 +1,332 @@ ?x ?label -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1002 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1008 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1014 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1021 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1026 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1031 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1037 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1042 -_:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid1048 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+_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid881 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid890 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid896 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid905 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid912 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid925 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid937 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid943 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid949 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid955 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid961 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid967 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid973 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid980 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid988 +_:Ba04bf4ddX2D70ecX2D4effX2Dbc56X2D3854fcd96d80genid994 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -372,9 +340,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "non-terminally differentiated cell" "myoblast" "fibroblast" - "ciliated cell" "epithelial cell" - "ciliated epithelial cell" "duct epithelial cell" "blood vessel endothelial cell" "non-branched duct epithelial cell" @@ -397,7 +363,6 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "mesodermal cell" "endodermal cell" "erythrocyte" - "brush border epithelial cell" "eukaryotic cell" "oxygen accumulating cell" "migratory neural crest cell" @@ -420,7 +385,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "supporting cell" "kidney granular cell" "mesangial cell" - "fenestrated cell" + "fenestrated endothelial cell" "pericyte" "muscle precursor cell" "somatic stem cell" @@ -492,13 +457,11 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "renal interstitial pericyte" "interstitial cell" "perivascular cell" - "microtubule cytoskeleton organization" "mitotic cell cycle" "nuclear division" "chromatin" "heterochromatin" "action potential" - "microtubule bundle formation" "formation of translation initiation ternary complex" "formation of primary germ layer" "ectoderm formation" @@ -540,16 +503,9 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "chromosome" "nucleolus" "cytoplasm" - "vacuole" - "Golgi apparatus" - "Golgi-associated vesicle" "ribosome" - "cytoskeleton" - "microtubule" "plasma membrane" "cell-cell junction" - "cilium" - "axoneme" "translation" "translational initiation" "translational elongation" @@ -557,14 +513,10 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "transport" "monoatomic ion transport" "water transport" - "vesicle targeting" "apoptotic process" "cellular component disassembly involved in execution phase of apoptosis" "muscle contraction" "organelle organization" - "cytoskeleton organization" - "microtubule-based process" - "microtubule-based movement" "cell cycle" "endomitotic cell cycle" "cell communication" @@ -597,17 +549,13 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "tissue development" "cellular process" "gene expression" - "transport along microtubule" "programmed cell death" - "endomembrane system" "protein transport" - "microtubule cytoskeleton" "gas transport" "oxygen transport" "membrane" "cellular component organization" "vesicle organization" - "vesicle-mediated transport" "morphogenesis of embryonic epithelium" "cell migration" "stem cell division" @@ -616,7 +564,6 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "sexual reproduction" "neural tube development" "cell cycle process" - "membrane docking" "cellular component disassembly" "reproductive process" "digestive system process" @@ -637,11 +584,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "apoptotic nuclear changes" "apoptotic chromosome condensation" "external encapsulating structure" - "cytoskeleton-dependent intracellular transport" - "intraciliary transport particle" "extracellular matrix" - "cytoplasmic vesicle" - "protein-containing complex localization" "membrane-enclosed lumen" "nuclear lumen" "vesicle" @@ -649,26 +592,20 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "bleb assembly" "multicellular organismal process" "developmental process" - "plasma membrane bounded cell projection cytoplasm" "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" "protein-DNA complex" "macromolecule localization" - "protein localization to organelle" "erythrocyte homeostasis" "monoatomic ion transmembrane transport" - "axoneme assembly" "tube formation" "tube morphogenesis" "tube development" "establishment of protein localization to extracellular region" - "intraciliary transport involved in cilium assembly" - "ciliary transition zone" "locomotion" "embryonic cleavage" "fluid transport" - "intraciliary transport" "regulation of membrane potential" "homeostatic process" "cell projection" @@ -690,14 +627,10 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "cellular metabolic process" "primary metabolic process" "cellular biosynthetic process" - "cilium organization" "establishment of protein localization" "synapse" "secretion" - "intracellular transport" "somatic stem cell division" - "Golgi vesicle transport" - "vesicle targeting, to, from or within Golgi" "organelle fission" "mesoderm morphogenesis" "cell development" @@ -725,20 +658,13 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "regulation of multicellular organismal process" "chromosome organization" "cell division" - "organelle localization" "cellular localization" - "vesicle localization" - "establishment of localization in cell" - "establishment of vesicle localization" - "establishment of organelle localization" "cellular response to stimulus" "transmembrane transport" "micturition" - "cilium assembly" "epithelium development" "epithelial tube morphogenesis" "morphogenesis of a branching epithelium" - "protein localization to cilium" "collagen-containing extracellular matrix" "protein-containing complex assembly" "biological regulation" @@ -752,22 +678,15 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "cellular macromolecule localization" "organelle assembly" "protein localization to extracellular region" - "organic substance transport" - "organic substance metabolic process" "protein-RNA complex organization" "cellular component organization or biogenesis" "cell periphery" "extracellular exosome assembly" "epithelial tube formation" - "ciliary plasm" "apoptotic signaling pathway" "execution phase of apoptosis" "renal filtration" "renal tubular secretion" - "microtubule bundle" - "intracellular vesicle" - "ciliary basal body-plasma membrane docking" - "vesicle targeting, trans-Golgi to periciliary membrane compartment" "extracellular exosome biogenesis" "plasma membrane region" "network-forming collagen trimer" @@ -780,24 +699,17 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "anterograde trans-synaptic signaling" "supramolecular complex" "supramolecular polymer" - "microtubule-based transport" - "supramolecular fiber" - "polymeric cytoskeletal fiber" "synaptic signaling" "trans-synaptic signaling" - "cytoplasmic region" "cellular anatomical entity" "plasma membrane bounded cell projection" "plasma membrane bounded cell projection assembly" "plasma membrane bounded cell projection organization" "mitotic nuclear division" - "organelle localization by membrane tethering" "extracellular vesicle biogenesis" "export from cell" - "organic substance biosynthetic process" "mitotic cell cycle process" "extracellular vesicle" - "ciliary transition zone assembly" "ribonucleoprotein complex" "root" "Muridae" @@ -864,14 +776,13 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "structure, cavities" "biconcave" "dendritic" + "fenestrated" "hollow" "basophilic" "laminar" "quality of a substance" - "subcylindrical" "3-D shape" "tubular" - "fiber shaped" "superelliptic" "acidophilic" "distensible" @@ -911,10 +822,12 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "renin" "sonic hedgehog protein" "T-cell acute lymphocytic leukemia protein 1" + "amino acid chain" "integrin alpha" "Mus musculus protein" "eukaryotic protein" "angiotensinogenase" + "protein-containing molecular entity" "processual entity" "tube" "appendage" @@ -1004,7 +917,7 @@ _:B17b7fe0dX2D5a3aX2D4b6fX2D8abfX2D380bcf1f27e6genid996 "primordium" "neural tube" "anatomical entity" - "posterior vena cava" + "inferior vena cava" "urine" "renal vein" "renal pelvis"